Fix formatting

Merge branch 'master' into relog-web
Add RELOG.version()
2025-12-06 15:48:51 -06:00 · 2023-02-15 13:47:00 -06:00 · 2023-02-15 13:27:47 -06:00 · 2023-02-15 13:22:47 -06:00 · 2023-02-15 12:32:29 -06:00 · 2023-02-15 11:01:10 -06:00
65 changed files with 1341 additions and 887 deletions
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -14,10 +14,10 @@ jobs:
        shell: julia --color=yes {0}
        run: |
          using Pkg
-          Pkg.add(PackageSpec(name="JuliaFormatter", version="0.14.4"))
+          Pkg.add(PackageSpec(name="JuliaFormatter", version="1"))
          using JuliaFormatter
          format("src", verbose=true)
-          format("test", verbose=true)
+          format("test/src", verbose=true)
          out = String(read(Cmd(`git diff`)))
          if isempty(out)
              exit(0)
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -10,7 +10,7 @@ jobs:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
-        version: ['1.3', '1.4', '1.5', '1.6']
+        version: ['1.6', '1.7', '1.8']
        os:
          - ubuntu-latest
        arch:
@@ -21,5 +21,15 @@ jobs:
        with:
          version: ${{ matrix.version }}
          arch: ${{ matrix.arch }}
-      - uses: julia-actions/julia-buildpkg@v1
-      - uses: julia-actions/julia-runtest@v1
+      - name: Run tests
+        shell: julia --color=yes --project=test {0}
+        run: |
+          using Pkg
+          Pkg.develop(path=".")
+          Pkg.update()
+          using RELOGT
+          try
+            runtests()
+          catch
+            exit(1)
+          end
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,39 +11,50 @@ All notable changes to this project will be documented in this file.
 [semver]: https://semver.org/spec/v2.0.0.html
 [pkjjl]: https://pkgdocs.julialang.org/v1/compatibility/#compat-pre-1.0

+## [0.6.0] -- 2022-12-15
+### Added
+- Allow RELOG to calculate approximate driving distances, instead of just straight-line distances between points.
+
+### Fixed
+- Fix bug that caused building period parameter to be ignored
+
+## [0.5.2] -- 2022-08-26
+### Changed
+- Update to JuMP 1.x
+
 ## [0.5.1] -- 2021-07-23
-## Added
+### Added
 - Allow user to specify locations as unique identifiers, instead of latitude and longitude (e.g. `us-state:IL` or `2018-us-county:17043`)
 - Add what-if scenarios.
 - Add products report.

 ## [0.5.0] -- 2021-01-06
-## Added
+### Added
 - Allow plants to store input material for processing in later years

 ## [0.4.0] -- 2020-09-18
-## Added
+### Added
 - Generate simplified solution reports (CSV)

 ## [0.3.3] -- 2020-10-13
-## Added
+### Added
 - Add option to write solution to JSON file in RELOG.solve
 - Improve error message when instance is infeasible
 - Make output file more readable

 ## [0.3.2] -- 2020-10-07
-## Added
+### Added
 - Add "building period" parameter

 ## [0.3.1] -- 2020-07-17
-## Fixed
+### Fixed
 - Fix expansion cost breakdown

 ## [0.3.0] -- 2020-06-25
-## Added
+### Added
 - Track emissions and energy (transportation and plants)

-## Changed
+### Changed
 - Minor changes to input file format:
    - Make all dictionary keys lowercase
    - Rename "outputs (tonne)" to "outputs (tonne/tonne)"
--- a/4
+++ b/4
@@ -1,5 +1,7 @@
 FROM julia:1.7-buster

+ENV RELOG_TIME_LIMIT_SEC=3600
+
 # Install Node.js & zip
 RUN apt-get update -yq && \
    apt-get -yq install curl gnupg ca-certificates && \
@@ -24,4 +26,4 @@ RUN julia --project=/app -e 'using Pkg; Pkg.precompile()'
 RUN cd /app/relog-web && npm run build

 WORKDIR /app
-CMD julia --project=/app -e 'import RELOG; RELOG.web("0.0.0.0")'
+CMD julia --project=/app -e 'import RELOG; RELOG.web("0.0.0.0")'
--- a/43
+++ b/43
@@ -1,32 +1,31 @@
-JULIA := julia --color=yes --project=@.
-SRC_FILES := $(wildcard src/*.jl test/*.jl)
-VERSION := 0.5
-
-all: docs test
-
-build/sysimage.so: src/sysimage.jl Project.toml Manifest.toml
-	mkdir -p build
-	$(JULIA) src/sysimage.jl
-
-build/test.log: $(SRC_FILES) build/sysimage.so
-	cd test; $(JULIA) --sysimage ../build/sysimage.so runtests.jl
+VERSION := 0.6
+PKG := ghcr.io/anl-ceeesa/relog-web

 clean:
-	rm -rf build/*
+	rm -rfv build Manifest.toml test/Manifest.toml deps/formatter/build deps/formatter/Manifest.toml

 docs:
-	mkdocs build -d ../docs/$(VERSION)/
-
+	cd docs; julia --project=. make.jl; cd ..
+	rsync -avP --delete-after docs/build/ ../docs/$(VERSION)/
+	
 docker-build:
-	docker build --tag relog:0.6 .
+	docker build --tag $(PKG):$(VERSION) .
+	docker build --tag $(PKG):latest .
+
+docker-push:
+	docker push $(PKG):$(VERSION)
+	docker push $(PKG):latest
+
+docker-run:
+	docker run -it --rm --name relog --volume $(PWD)/jobs:/app/jobs --publish 8000:8080 $(PKG):$(VERSION)

 format:
-	julia -e 'using JuliaFormatter; format(["src", "test"], verbose=true);'
+	cd deps/formatter; ../../juliaw format.jl

-test: build/test.log
+test: test/Manifest.toml
+	./juliaw test/runtests.jl

-test-watch:
-	bash -c "while true; do make test --quiet; sleep 1; done"
-
-.PHONY: docs test
+test/Manifest.toml: test/Project.toml
+	julia --project=test -e "using Pkg; Pkg.instantiate()"

+.PHONY: docs test format
--- a/Project.toml
+++ b/Project.toml
@@ -1,13 +1,11 @@
 name = "RELOG"
 uuid = "a2afcdf7-cf04-4913-85f9-c0d81ddf2008"
 authors = ["Alinson S Xavier <axavier@anl.gov>"]
-version = "0.5.1"
+version = "0.6.0"

 [deps]
 CRC = "44b605c4-b955-5f2b-9b6d-d2bd01d3d205"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
-Cbc = "9961bab8-2fa3-5c5a-9d89-47fab24efd76"
-Clp = "e2554f3b-3117-50c0-817c-e040a3ddf72d"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
@@ -15,13 +13,14 @@ Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 GZip = "92fee26a-97fe-5a0c-ad85-20a5f3185b63"
 Geodesy = "0ef565a4-170c-5f04-8de2-149903a85f3d"
 HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
+HiGHS = "87dc4568-4c63-4d18-b0c0-bb2238e4078b"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 JSONSchema = "7d188eb4-7ad8-530c-ae41-71a32a6d4692"
 JuMP = "4076af6c-e467-56ae-b986-b466b2749572"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MathOptInterface = "b8f27783-ece8-5eb3-8dc8-9495eed66fee"
+NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
-PackageCompiler = "9b87118b-4619-50d2-8e1e-99f35a4d4d9d"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 ProgressBars = "49802e3a-d2f1-5c88-81d8-b72133a6f568"
@@ -33,21 +32,19 @@ ZipFile = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea"

 [compat]
 CRC = "4"
-CSV = "0.7"
-Cbc = "0.6"
-Clp = "0.8"
-DataFrames = "0.21"
-DataStructures = "0.17"
+CSV = "0.10"
+DataFrames = "1"
+DataStructures = "0.18"
 GZip = "0.5"
-Geodesy = "0.5"
+Geodesy = "1"
 HTTP = "0.9"
 JSON = "0.21"
-JSONSchema = "0.3"
-JuMP = "0.21"
-MathOptInterface = "0.9"
-OrderedCollections = "1.4"
-PackageCompiler = "1"
-ProgressBars = "0.6"
-Shapefile = "0.7"
-ZipFile = "0.9"
+JSONSchema = "1"
+JuMP = "1"
+MathOptInterface = "1"
+NearestNeighbors = "0.4"
+OrderedCollections = "1"
+ProgressBars = "1"
+Shapefile = "0.8"
+ZipFile = "0.10"
 julia = "1"
--- a/README.md
+++ b/README.md
@@ -13,22 +13,24 @@

 **RELOG** is a supply chain optimization package focusing on reverse logistics and reverse manufacturing. For example, the package can be used to determine where to build recycling plants, what sizes should they have and which customers should be served by which plants. The package supports customized reverse logistics pipelines, with multiple types of plants, multiple types of product and multiple time periods.

-<img src="https://anl-ceeesa.github.io/RELOG/0.5/images/ex_transportation.png" width="1000px"/>
+
+
+<img src="https://anl-ceeesa.github.io/RELOG/0.6/assets/ex_transportation.png" width="1000px"/>

 ### Documentation

- [Usage](https://anl-ceeesa.github.io/RELOG/0.5/usage)
- [Input and Output Data Formats](https://anl-ceeesa.github.io/RELOG/0.5/format)
- [Simplified Solution Reports](https://anl-ceeesa.github.io/RELOG/0.5/reports)
- [Optimization Model](https://anl-ceeesa.github.io/RELOG/0.5/model)
+  * [Usage](https://anl-ceeesa.github.io/RELOG/0.6/usage)
+  * [Input and Output Data Formats](https://anl-ceeesa.github.io/RELOG/0.6/format)
+  * [Simplified Solution Reports](https://anl-ceeesa.github.io/RELOG/0.6/reports)
+  * [Optimization Model](https://anl-ceeesa.github.io/RELOG/0.6/model)

 ### Authors

- **Alinson S. Xavier** <<axavier@anl.gov>>
- **Nwike Iloeje** <<ciloeje@anl.gov>>
- **John Atkins**
- **Kyle Sun**
- **Audrey Gallier**
+* **Alinson S. Xavier** <<axavier@anl.gov>>
+* **Nwike Iloeje** <<ciloeje@anl.gov>>
+* **John Atkins**
+* **Kyle Sun**
+* **Audrey Gallier**

 ### License

--- a/docs/Project.toml
+++ b/docs/Project.toml
@@ -0,0 +1,4 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+RELOG = "a2afcdf7-cf04-4913-85f9-c0d81ddf2008"
+Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
--- a/docs/make.jl
+++ b/docs/make.jl
@@ -0,0 +1,19 @@
+using Documenter, RELOG
+
+function make()
+    makedocs(
+        sitename="RELOG",
+        pages=[
+            "Home" => "index.md",
+            "usage.md",
+            "format.md",
+            "reports.md",
+            "model.md",
+        ],
+        format = Documenter.HTML(
+            assets=["assets/custom.css"],
+        )
+    )
+end
+
+make()
--- a/docs/src/assets/custom.css
+++ b/docs/src/assets/custom.css
@@ -0,0 +1,36 @@
+@media screen and (min-width: 1056px) {
+    #documenter .docs-main {
+      max-width: 65rem !important;
+    }
+}
+  
+
+tbody, thead, pre {
+    border: 1px solid rgba(0, 0, 0, 0.25);
+}
+
+table td, th {
+    padding: 8px;
+}
+
+table p {
+    margin-bottom: 0;
+}
+
+table td code {
+    white-space: nowrap;
+}
+
+table tr,
+table th {
+    border-bottom: 1px solid rgba(0, 0, 0, 0.1);
+}
+
+table tr:last-child {
+    border-bottom: 0;
+}
+
+code {
+    background-color: transparent;
+    color: rgb(232, 62, 140);
+}
--- a/docs/src/assets/ex_amount_produced.png
+++ b/docs/src/assets/ex_amount_produced.png
--- a/docs/src/assets/ex_emissions.png
+++ b/docs/src/assets/ex_emissions.png
--- a/docs/src/assets/ex_plant_cost_per_year.png
+++ b/docs/src/assets/ex_plant_cost_per_year.png
--- a/docs/src/assets/ex_plant_locations.png
+++ b/docs/src/assets/ex_plant_locations.png
--- a/docs/src/assets/ex_transportation.png
+++ b/docs/src/assets/ex_transportation.png
--- a/docs/src/assets/ex_transportation_amount_distance.png
+++ b/docs/src/assets/ex_transportation_amount_distance.png
--- a/docs/src/assets/ex_transportation_emissions.png
+++ b/docs/src/assets/ex_transportation_emissions.png
--- a/docs/src/format.md
+++ b/docs/src/format.md
@@ -11,9 +11,10 @@ RELOG accepts as input a JSON file with three sections: `parameters`, `products`
 The **parameters** section describes details about the simulation itself.

 | Key                       | Description
-|:--------------------------|---------------|
+|:--------------------------|:---------------|
 |`time horizon (years)`     | Number of years in the simulation.
 |`building period (years)`  | List of years in which we are allowed to open new plants. For example, if this parameter is set to `[1,2,3]`, we can only open plants during the first three years. By default, this equals `[1]`; that is, plants can only be opened during the first year. |
+|`distance metric` | Metric used to compute distances between pairs of locations. Valid options are: `"Euclidean"`, for the straight-line distance between points; or `"driving"` for an approximated driving distance. If not specified, defaults to `"Euclidean"`.


 #### Example
@@ -21,7 +22,8 @@ The **parameters** section describes details about the simulation itself.
 {
    "parameters": {
        "time horizon (years)": 2,
-        "building period (years)": [1]
+        "building period (years)": [1],
+        "distance metric": "driving",
    }
 }
 ```
@@ -31,16 +33,18 @@ The **parameters** section describes details about the simulation itself.
 The **products** section describes all products and subproducts in the simulation. The field `instance["Products"]` is a dictionary mapping the name of the product to a dictionary which describes its characteristics. Each product description contains the following keys:

 | Key                                   | Description
-|:--------------------------------------|---------------|
+|:--------------------------------------|:---------------|
 |`transportation cost ($/km/tonne)`     | The cost to transport this product. Must be a time series.
 |`transportation energy (J/km/tonne)`   | The energy required to transport this product. Must be a time series. Optional.
 |`transportation emissions (tonne/km/tonne)`  | A dictionary mapping the name of each greenhouse gas, produced to transport one tonne of this product along one kilometer, to the amount of gas produced (in tonnes). Must be a time series. Optional.
 |`initial amounts`                      | A dictionary mapping the name of each location to its description (see below). If this product is not initially available, this key may be omitted. Must be a time series.
+| `disposal limit (tonne)`              | Total amount of product that can be disposed of across all collection centers. If omitted, all product must be processed. This parameter has no effect on product disposal at plants.
+| `disposal cost ($/tonne)`              | Cost of disposing one tonne of this product at a collection center. If omitted, defaults to zero. This parameter has no effect on product disposal costs at plants.

 Each product may have some amount available at the beginning of each time period. In this case, the key `initial amounts` maps to a dictionary with the following keys:

 | Key                     | Description
-|:------------------------|---------------|
+|:------------------------|:---------------|
 | `latitude (deg)`        | The latitude of the location.
 | `longitude (deg)`       | The longitude of the location.
 | `amount (tonne)`       | The amount of the product initially available at the location. Must be a time series.
@@ -73,7 +77,9 @@ Each product may have some amount available at the beginning of each time period
            "transportation emissions (tonne/km/tonne)": {
                "CO2": [0.052, 0.050],
                "CH4": [0.003, 0.002]
-            }
+            },
+            "disposal cost ($/tonne)": [-10.0, -12.0],
+            "disposal limit (tonne)": [1.0, 1.0],
        },
        "P2": {
            "transportation cost ($/km/tonne)": [0.022, 0.020]
@@ -93,7 +99,7 @@ Each product may have some amount available at the beginning of each time period
 The **plants** section describes the available types of reverse manufacturing plants, their potential locations and associated costs, as well as their inputs and outputs. The field `instance["Plants"]` is a dictionary mapping the name of the plant to a dictionary with the following keys:

 | Key                     | Description
-|:------------------------|---------------|
+|:------------------------|:---------------|
 | `input`                 | The name of the product that this plant takes as input. Only one input is accepted per plant.
 | `outputs (tonne/tonne)`               | A dictionary specifying how many tonnes of each product is produced for each tonnes of input. For example, if the plant outputs 0.5 tonnes of P2 and 0.25 tonnes of P3 for each tonnes of P1 provided, then this entry should be `{"P2": 0.5, "P3": 0.25}`. If the plant does not output anything, this key may be omitted.
 |`energy (GJ/tonne)`   | The energy required to process 1 tonne of the input. Must be a time series. Optional.
@@ -113,14 +119,14 @@ Each type of plant is associated with a set of potential locations where it can
 The `storage` dictionary should contain the following keys:

 | Key                     | Description
-|:------------------------|---------------|
+|:------------------------|:---------------|
 | `cost ($/tonne)`       | The cost to store a tonne of input product for one time period. Must be a time series.
 | `limit (tonne)`        | The maximum amount of input product this plant can have in storage at any given time.

 The keys in the `disposal` dictionary should be the names of the products. The values are dictionaries with the following keys:

 | Key                     | Description
-|:------------------------|---------------|
+|:------------------------|:---------------|
 | `cost ($/tonne)`       | The cost to dispose of the product. Must be a time series.
 | `limit (tonne)`        | The maximum amount that can be disposed of. If an unlimited amount can be disposed, this key may be omitted. Must be a time series.

@@ -128,7 +134,7 @@ The keys in the `disposal` dictionary should be the names of the products. The v
 The keys in the `capacities (tonne)` dictionary should be the amounts (in tonnes). The values are dictionaries with the following keys:

 | Key                                   | Description
-|:--------------------------------------|---------------|
+|:--------------------------------------|:---------------|
 | `opening cost ($)`                    | The cost to open a plant of this size.
 | `fixed operating cost ($)`            | The cost to keep the plant open, even if the plant doesn't process anything. Must be a time series.
 | `variable operating cost ($/tonne)`  | The cost that the plant incurs to process each tonne of input. Must be a time series.
@@ -210,7 +216,7 @@ is is possible to write:
 Location names follow the format `db:id`, where `db` is the name of the database and `id` is the identifier for a specific location. RELOG currently includes the following databases:

 Database | Description | Examples
---------|-------------|----------
+:--------|:------------|:---------
 `us-state`| List of states of the United States. | `us-state:IL` (State of Illinois)
 `2018-us-county` | List of United States counties, as of 2018. IDs are 5-digit FIPS codes. | `2018-us-county:17043` (DuPage county in Illinois)

@@ -220,6 +226,7 @@ Database | Description | Examples
 * Plants can be expanded at any time, even long after they are open.
 * All material available at the beginning of a time period must be entirely processed by the end of that time period. It is not possible to store unprocessed materials from one time period to the next.
 * Up to two plant sizes are currently supported. Variable operating costs must be the same for all plant sizes.
+* Accurate driving distances are only available for the continental United States.

 ## Output Data Format (JSON)

--- a/docs/src/index.md
+++ b/docs/src/index.md
@@ -1,25 +1,29 @@
 # RELOG: Reverse Logistics Optimization

-
 **RELOG** is an open-source supply chain optimization package focusing on reverse logistics and reverse manufacturing. The package uses Mixed-Integer Linear Programming to determine where to build recycling plants, what size should these plants have and which customers should be served by which plants. The package supports custom reverse logistics pipelines, with multiple types of plants, multiple types of product and multiple time periods.

-<img src="images/ex_transportation.png" width="1000px"/>
+```@raw html
+<center>
+   <img src="assets/ex_transportation.png" width="1000px"/>
+</center>
+```


 ### Table of Contents

-  * [Usage](usage.md)
-  * [Input and Output Data Formats](format.md)
-  * [Simplified Solution Reports](reports.md)
-  * [Optimization Model](model.md)
+  ```@contents
+Pages = ["usage.md", "format.md", "reports.md", "model.md"]
+Depth = 3
+```
+
  
 ### Source Code

  * [https://github.com/ANL-CEEESA/RELOG](https://github.com/ANL-CEEESA/RELOG)

 ### Authors
-* **Alinson S. Xavier,** Argonne National Laboratory <<axavier@anl.gov>>
-* **Nwike Iloeje,** Argonne National Laboratory <<ciloeje@anl.gov>>
+* **Alinson S. Xavier,** Argonne National Laboratory <axavier@anl.gov>
+* **Nwike Iloeje,** Argonne National Laboratory <ciloeje@anl.gov>

 ### License

--- a/docs/src/model.md
+++ b/docs/src/model.md
@@ -6,53 +6,65 @@ In this page, we describe the precise mathematical optimization model used by RE

 ### Sets

-* $L$ - Set of locations holding the original material to be recycled
-* $M$ - Set of materials recovered during the reverse manufacturing process
-* $P$ - Set of potential plants to open
-* $T = \{ 1, \ldots, t^{max} \} $ - Set of time periods
+Symbol | Description
+:-------|:------------
+$L$ | Set of locations holding the original material to be recycled
+$M$ | Set of materials recovered during the reverse manufacturing process
+$P$ | Set of potential plants to open
+$T = \{ 1, \ldots, t^{max} \}$ | Set of time periods

 ### Constants

-**Plants:**
+#### Plants

-* $c^\text{disp}_{pmt}$ - Cost of disposing one tonne of material $m$ at plant $p$ during time $t$ (`$/tonne/km`)
-* $c^\text{exp}_{pt}$ - Cost of adding one tonne of capacity to plant $p$ at time $t$ (`$/tonne`)
-* $c^\text{open}_{pt}$ - Cost of opening plant $p$ at time $t$, at minimum capacity (`$`)
-* $c^\text{f-base}_{pt}$ - Fixed cost of keeping plant $p$ open during time period $t$ (`$`)
-* $c^\text{f-exp}_{pt}$ - Increase in fixed cost for each additional tonne of capacity (`$/tonne`)
-* $c^\text{var}_{pt}$ - Variable cost of processing one tonne of input at plant $p$ at time $t$ (`$/tonne`)
-* $c^\text{store}_{pt}$ - Cost of storing one tonne of original material at plant $p$ at time $t$ (`$/tonne`)
-* $m^\text{min}_p$ - Minimum capacity of plant $p$ (`tonne`)
-* $m^\text{max}_p$ - Maximum capacity of plant $p$ (`tonne`)
-* $m^\text{disp}_{pmt}$ - Maximum amount of material $m$ that plant $p$ can dispose of during time $t$ (`tonne`)
-* $m^\text{store}_p$ - Maximum amount of original material that plant $p$ can store for later processing.
+Symbol | Description | Unit
+:-------|:------------|:---
+$c^\text{disp}_{pmt}$ | Cost of disposing one tonne of material $m$ at plant $p$ during time $t$ | \$/tonne/km
+$c^\text{exp}_{pt}$ | Cost of adding one tonne of capacity to plant $p$ at time $t$ | \$/tonne
+$c^\text{open}_{pt}$ | Cost of opening plant $p$ at time $t$, at minimum capacity | $
+$c^\text{f-base}_{pt}$ | Fixed cost of keeping plant $p$ open during time period $t$ | $
+$c^\text{f-exp}_{pt}$ | Increase in fixed cost for each additional tonne of capacity | \$/tonne
+$c^\text{var}_{pt}$ | Variable cost of processing one tonne of input at plant $p$ at time $t$ | \$/tonne
+$c^\text{store}_{pt}$ | Cost of storing one tonne of original material at plant $p$ at time $t$ | \$/tonne
+$m^\text{min}_p$ | Minimum capacity of plant $p$ | tonne
+$m^\text{max}_p$ | Maximum capacity of plant $p$ | tonne
+$m^\text{disp}_{pmt}$ | Maximum amount of material $m$ that plant $p$ can dispose of during time $t$ | tonne
+$m^\text{store}_p$ | Maximum amount of original material that plant $p$ can store for later processing. | tonne

-**Products:**
+#### Products

-* $\alpha_{pm}$ - Amount of material $m$ recovered by plant $t$ for each tonne of original material (`tonne/tonne`)
-* $m^\text{initial}_{lt}$ - Amount of original material to be recycled at location $l$ during time $t$ (`tonne`)
+Symbol | Description | Unit
+:-------|:------------|:---
+$\alpha_{pm}$ | Amount of material $m$ recovered by plant $t$ for each tonne of original material | tonne/tonne
+$m^\text{initial}_{lt}$ | Amount of original material to be recycled at location $l$ during time $t$ | tonne

-**Transportation:**
+#### Transportation

-* $c^\text{tr}_{t}$ - Transportation cost during time $t$ (`$/tonne/km`)
-* $d_{lp}$ - Distance between plant $p$ and location $l$ (`km`)
+Symbol | Description | Unit
+:-------|:------------|:---
+$c^\text{tr}_{t}$ | Transportation cost during time $t$ | \$/tonne/km
+$d_{lp}$ | Distance between plant $p$ and location $l$ | km


 ### Decision variables
-* $q_{mpt}$ - Amount of material $m$ recovered by plant $p$ during time $t$ (`tonne`)
-* $u_{pt}$ - Binary variable that equals 1 if plant $p$ starts operating at time $t$ (`bool`)
-* $w_{pt}$ - Extra capacity (amount above the minimum) added to plant $p$ during time $t$ (`tonne`)
-* $x_{pt}$ - Binary variable that equals 1 if plant $p$ is operational at time $t$ (`bool`)
-* $y_{lpt}$ - Amount of product sent from location $l$ to plant $p$ during time $t$ (`tonne`)
-* $z^{\text{disp}}_{mpt}$ - Amount of material $m$ disposed of by plant $p$ during time $t$ (`tonne`)
-* $z^{\text{store}}_{pt}$ - Amount of original material in storage at plant $p$ by the end of time period $t$ (`tonne`)
-* $z^{\text{proc}}_{mpt}$ - Amount of original material processed by plant $p$ during time period $t$ (`tonne`)
+
+Symbol | Description | Unit
+:-------|:------------|:---
+$q_{mpt}$ | Amount of material $m$ recovered by plant $p$ during time $t$ | tonne
+$u_{pt}$ | Binary variable that equals 1 if plant $p$ starts operating at time $t$ | Boolean
+$w_{pt}$ | Extra capacity (amount above the minimum) added to plant $p$ during time $t$ | tonne
+$x_{pt}$ | Binary variable that equals 1 if plant $p$ is operational at time $t$ | Boolean
+$y_{lpt}$ | Amount of product sent from location $l$ to plant $p$ during time $t$ | tonne
+$z^{\text{disp}}_{mpt}$ | Amount of material $m$ disposed of by plant $p$ during time $t$ | tonne
+$z^{\text{store}}_{pt}$ | Amount of original material in storage at plant $p$ by the end of time period $t$ | tonne
+$z^{\text{proc}}_{mpt}$ | Amount of original material processed by plant $p$ during time period $t$ | tonne


 ### Objective function

 RELOG minimizes the overall capital, production and transportation costs:

+```math
 \begin{align*}
    \text{minimize} \;\; &
        \sum_{t \in T} \sum_{p \in P} \left[
@@ -73,6 +85,7 @@ RELOG minimizes the overall capital, production and transportation costs:
    &
        \sum_{t \in T} \sum_{p \in P} \sum_{m \in M} c^{\text{disp}}_{pmt} z_{pmt}
 \end{align*}
+```

 In the first line, we have (i) opening costs, if plant starts operating at time $t$, (ii) fixed operating costs, if plant is operational, (iii) additional fixed operating costs coming from expansion performed in all previous time periods up to the current one, and finally (iv) the expansion costs during the current time period.
 In the second line, we have storage and variable processing costs.
@@ -83,14 +96,17 @@ In the fourth line, we have the disposal costs.

 * All original materials must be sent to a plant:

-\begin{align}
+```math
+\begin{align*}
    & \sum_{p \in P} y_{lpt} = m^\text{initial}_{lt} 
        & \forall l \in L, t \in T
-\end{align}
+\end{align*}
+```

 * Amount received equals amount processed plus stored. Furthermore, all original material should be processed by the end of the simulation.

-\begin{align}
+```math
+\begin{align*}
    & \sum_{l \in L} y_{lpt} + z^{\text{store}}_{p,t-1}
        = z^{\text{proc}}_{pt} + z^{\text{store}}_{p,t}
        & \forall p \in P, t \in T \\
@@ -98,56 +114,70 @@ In the fourth line, we have the disposal costs.
        & \forall p \in P \\
    & z^{\text{store}}_{p,t^{\max}} = 0
        & \forall p \in P
-\end{align}
+\end{align*}
+```

 * Plants have a limited processing capacity. Furthermore, if a plant is closed, it has zero processing capacity:

-\begin{align}
+```math
+\begin{align*}
    & z^{\text{proc}}_{pt} \leq m^\text{min}_p x_p + \sum_{i=1}^t w_p
        & \forall p \in P, t \in T
-\end{align}
+\end{align*}
+```

 * Plants have limited storage capacity. Furthermore, if a plant is closed, is has zero storage capacity:

-\begin{align}
+```math
+\begin{align*}
    & z^{\text{store}}_{pt} \leq m^\text{store}_p x_p
        & \forall p \in P, t \in T
-\end{align}
+\end{align*}
+```

 * Plants can only be expanded up to their maximum capacity. Furthermore, if a plant is closed, it cannot be expanded:

-\begin{align}
+```math
+\begin{align*}
    & \sum_{i=1}^t w_p \leq m^\text{max}_p x_p
        & \forall p \in P, t \in T
-\end{align}
+\end{align*}
+```

 * Amount of recovered material is proportional to amount processed: 

-\begin{align}
+```math
+\begin{align*}
    & q_{mpt} = \alpha_{pm} z^{\text{proc}}_{pt}
        & \forall m \in M, p \in P, t \in T
-\end{align}
+\end{align*}
+```

 * Because we only consider a single type of plant, all recovered material must be immediately disposed of. In RELOG's full model, recovered materials may be sent to another plant for further processing.

-\begin{align}
+```math
+\begin{align*}
    & q_{mpt} = z_{mpt}
        & \forall m \in M, p \in P, t \in T
-\end{align}
+\end{align*}
+```

 * A plant is operational at time $t$ if it was operational at time $t-1$ or it was built at time $t$. This constraint also prevents a plant from being built multiple times.

-\begin{align}
+```math
+\begin{align*}
    & x_{pt} = x_{p,t-1} + u_{pt}
        & \forall p \in P, t \in T \setminus \{1\} \\
    & x_{p,1} = u_{p,1}
        & \forall p \in P
-\end{align}
+\end{align*}
+```


 * Variable bounds:

-\begin{align}
+```math
+\begin{align*}
    & q_{mpt} \geq 0
        & \forall m \in M, p \in P, t \in T \\
    & u_{pt} \in \{0,1\}
@@ -162,4 +192,5 @@ In the fourth line, we have the disposal costs.
        & p \in P, t \in T \\
    & z^{\text{disp}}_{mpt}, z^{\text{proc}}_{mpt} \geq 0
        & \forall m \in M, p \in P, t \in T
-\end{align}
+\end{align*}
+```
--- a/docs/src/reports.md
+++ b/docs/src/reports.md
@@ -9,7 +9,7 @@ In this page, we also illustrate what types of charts and visualizations can be
 Report showing plant costs, capacities, energy expenditure and utilization factors. Generated by `RELOG.write_plants_report(solution, filename)`.

 | Column                                | Description
-|:--------------------------------------|---------------|
+|:--------------------------------------|:---------------|
 | `plant type` | Plant type.
 | `location name` | Location name.
 | `year` | What year this row corresponds to. This reports includes one row for each year.
@@ -45,7 +45,9 @@ sns.barplot(x="year",
                     .reset_index());
 ```

-<img src="../images/ex_plant_cost_per_year.png" width="500px"/>
+```@raw html
+<img src="../assets/ex_plant_cost_per_year.png" width="500px"/>
+```

 * Map showing plant locations (in Python):
 ```python
@@ -65,8 +67,9 @@ points = gp.points_from_xy(data["longitude (deg)"],
 gp.GeoDataFrame(data, geometry=points).plot(ax=ax);
 ```

-<img src="../images/ex_plant_locations.png" width="1000px"/>
-
+```@raw html
+<img src="../assets/ex_plant_locations.png" width="1000px"/>
+```

 ## Plant outputs report

@@ -74,7 +77,7 @@ Report showing amount of products produced, sent and disposed of by each plant,


 | Column                                | Description
-|:--------------------------------------|---------------|
+|:--------------------------------------|:---------------|
 | `plant type`  | Plant type.
 | `location name`  | Location name.
 | `year`  | What year this row corresponds to. This reports includes one row for each year.
@@ -101,7 +104,9 @@ sns.barplot(x="amount produced (tonne)",
                     .reset_index());
 ```

-<img src="../images/ex_amount_produced.png" width="500px"/>
+```@raw html
+<img src="../assets/ex_amount_produced.png" width="500px"/>
+```


 ## Plant emissions report
@@ -109,7 +114,7 @@ sns.barplot(x="amount produced (tonne)",
 Report showing amount of emissions produced by each plant. Generated by `RELOG.write_plant_emissions_report(solution, filename)`.

 | Column                                | Description
-|:--------------------------------------|---------------|
+|:--------------------------------------|:---------------|
 | `plant type` | Plant type.
 | `location name` | Location name.
 | `year` | Year.
@@ -133,20 +138,23 @@ sns.barplot(x="plant type",
                     .reset_index());
 ```

-<img src="../images/ex_emissions.png" width="500px"/>
+```@raw html
+<img src="../assets/ex_emissions.png" width="500px"/>
+```

 ## Products report

 Report showing primary product amounts, locations and marginal costs. Generated by `RELOG.write_products_report(solution, filename)`.

 | Column                                | Description
-|:--------------------------------------|---------------|
+|:--------------------------------------|:---------------|
 | `product name`  | Product name.
 | `location name`  | Name of the collection center.
 | `latitude (deg)` | Latitude of the collection center.
 | `longitude (deg)` | Longitude of the collection center.
 | `year`  | What year this row corresponds to. This reports includes one row for each year.
 | `amount (tonne)` | Amount of product available at this collection center.
+| `amount disposed (tonne)` | Amount of product disposed of at this collection center.
 | `marginal cost ($/tonne)` | Cost to process one additional tonne of this product coming from this collection center.


@@ -156,7 +164,7 @@ Report showing amount of product sent from initial locations to plants, and from


 | Column                                | Description
-|:--------------------------------------|---------------|
+|:--------------------------------------|:---------------|
 | `source type` | If product is being shipped from an initial location, equals `Origin`. If product is being shipped from a plant, equals plant type.
 | `source location name` | Name of the location where the product is being shipped from.
 | `source latitude (deg)` | Latitude of the source location.
@@ -190,7 +198,9 @@ sns.barplot(x="product",
                     .reset_index());
 ```

-<img src="../images/ex_transportation_amount_distance.png" width="500px"/>
+```@raw html
+<img src="../assets/ex_transportation_amount_distance.png" width="500px"/>
+```

 * Map of transportation lines (in Python):

@@ -233,7 +243,9 @@ gp.GeoDataFrame(data, geometry=points).plot(ax=ax,
                                            markersize=50);
 ```

-<img src="../images/ex_transportation.png" width="1000px"/>
+```@raw html
+<img src="../assets/ex_transportation.png" width="1000px"/>
+```


 ## Transportation emissions report
@@ -241,7 +253,7 @@ gp.GeoDataFrame(data, geometry=points).plot(ax=ax,
 Report showing emissions for each trip between initial locations and plants, and between pairs of plants. Generated by `RELOG.write_transportation_emissions_report(solution, filename)`.

 | Column                                | Description
-|:--------------------------------------|---------------|
+|:--------------------------------------|:---------------|
 | `source type` | If product is being shipped from an initial location, equals `Origin`. If product is being shipped from a plant, equals plant type.
 | `source location name` | Name of the location where the product is being shipped from.
 | `source latitude (deg)` | Latitude of the source location.
@@ -275,4 +287,6 @@ sns.barplot(x="emission type",
                     .reset_index());
 ```

-<img src="../images/ex_transportation_emissions.png" width="500px"/>
+```@raw html
+<img src="../assets/ex_transportation_emissions.png" width="500px"/>
+```
--- a/docs/src/usage.md
+++ b/docs/src/usage.md
@@ -3,22 +3,11 @@ Usage

 ## 1. Installation

-To use RELOG, the first step is to install the [Julia programming language](https://julialang.org/) on your machine. Note that RELOG was developed and tested with Julia 1.5 and may not be compatible with newer versions. After Julia is installed, launch the Julia console, type `]` to switch to package manger mode, then run:
+To use RELOG, the first step is to install the [Julia programming language](https://julialang.org/) on your machine. Note that RELOG was developed and tested with Julia 1.8 and may not be compatible with newer versions. After Julia is installed, launch the Julia console, then run:

-```text
-(@v1.5) pkg> add https://github.com/ANL-CEEESA/RELOG.git
-```
-
-After the package and all its dependencies have been installed, please run the RELOG test suite, as shown below, to make sure that the package has been correctly installed:
-
-```text
-(@v1.5) pkg> test RELOG
-```
-
-To update the package to a newer version, type `]` to enter the package manager mode, then run:
-
-```text
-(@v1.5) pkg> update RELOG
+```julia
+using Pkg
+Pkg.add(name="RELOG", version="0.6")
 ```

 ## 2. Modeling the problem
@@ -106,18 +95,22 @@ To use the `resolve` method, the new input file should be very similar to the or

 ### 5.1 Changing the solver

-By default, RELOG internally uses [Cbc](https://github.com/coin-or/Cbc), an open-source and freely-available Mixed-Integer Linear Programming solver developed by the [COIN-OR Project](https://www.coin-or.org/). For larger-scale test cases, a commercial solver such as Gurobi, CPLEX or XPRESS is recommended. The following snippet shows how to switch from Cbc to Gurobi, for example:
+By default, RELOG internally uses [HiGHS](https://github.com/ERGO-Code/HiGHS), an open-source and freely-available Mixed-Integer Linear Programming solver. For larger-scale test cases, a commercial solver such as Gurobi, CPLEX or XPRESS is recommended. The following snippet shows how to switch to Gurobi, for example:

 ```julia
 using RELOG, Gurobi, JuMP

-gurobi = optimizer_with_attributes(Gurobi.Optimizer,
-                                   "TimeLimit" => 3600,
-                                   "MIPGap" => 0.001)
+gurobi = optimizer_with_attributes(
+    Gurobi.Optimizer,
+    "TimeLimit" => 3600,
+    "MIPGap" => 0.001,
+)

-RELOG.solve("instance.json",
-            output="solution.json",
-            optimizer=gurobi)
+RELOG.solve(
+    "instance.json",
+    output="solution.json",
+    optimizer=gurobi,
+)
 ```

 ### 5.2 Multi-period heuristics
@@ -133,6 +126,8 @@ To solve an instance using this heuristic, use the option `heuristic=true`, as s
 ```julia
 using RELOG

-solution = RELOG.solve("/home/user/instance.json",
-                       heuristic=true)
+solution = RELOG.solve(
+    "/home/user/instance.json",
+    heuristic=true,
+)
 ```
--- a/instances/s1.json
+++ b/instances/s1.json
@@ -1,202 +0,0 @@
-{
-    "parameters": {
-        "time horizon (years)": 2
-    },
-    "products": {
-        "P1": {
-            "transportation cost ($/km/tonne)": [0.015, 0.015],
-            "transportation energy (J/km/tonne)": [0.12, 0.11],
-            "transportation emissions (tonne/km/tonne)": {
-                "CO2": [0.052, 0.050],
-                "CH4": [0.003, 0.002]
-            },            
-            "initial amounts": {
-                "C1": {
-                    "latitude (deg)": 7.0,
-                    "longitude (deg)": 7.0,
-                    "amount (tonne)": [934.56, 934.56]
-                },
-                "C2": {
-                    "latitude (deg)": 7.0,
-                    "longitude (deg)": 19.0,
-                    "amount (tonne)": [198.95, 198.95]
-                },
-                "C3": {
-                    "latitude (deg)": 84.0,
-                    "longitude (deg)": 76.0,
-                    "amount (tonne)": [212.97, 212.97]
-                },
-                "C4": {
-                    "latitude (deg)": 21.0,
-                    "longitude (deg)": 16.0,
-                    "amount (tonne)": [352.19, 352.19]
-                },
-                "C5": {
-                    "latitude (deg)": 32.0,
-                    "longitude (deg)": 92.0,
-                    "amount (tonne)": [510.33, 510.33]
-                },
-                "C6": {
-                    "latitude (deg)": 14.0,
-                    "longitude (deg)": 62.0,
-                    "amount (tonne)": [471.66, 471.66]
-                },
-                "C7": {
-                    "latitude (deg)": 30.0,
-                    "longitude (deg)": 83.0,
-                    "amount (tonne)": [785.21, 785.21]
-                },
-                "C8": {
-                    "latitude (deg)": 35.0,
-                    "longitude (deg)": 40.0,
-                    "amount (tonne)": [706.17, 706.17]
-                },
-                "C9": {
-                    "latitude (deg)": 74.0,
-                    "longitude (deg)": 52.0,
-                    "amount (tonne)": [30.08, 30.08]
-                },
-                "C10": {
-                    "latitude (deg)": 22.0,
-                    "longitude (deg)": 54.0,
-                    "amount (tonne)": [536.52, 536.52]
-                }
-            }
-        },
-        "P2": {
-            "transportation cost ($/km/tonne)": [0.02, 0.02]
-        },
-        "P3": {
-            "transportation cost ($/km/tonne)": [0.0125, 0.0125]
-        },
-        "P4": {
-            "transportation cost ($/km/tonne)": [0.0175, 0.0175]
-        }
-    },
-    "plants": {
-        "F1": {
-            "input": "P1",
-            "outputs (tonne/tonne)": {
-                "P2": 0.2,
-                "P3": 0.5
-            },
-            "energy (GJ/tonne)": [0.12, 0.11],
-            "emissions (tonne/tonne)": {
-                "CO2": [0.052, 0.050],
-                "CH4": [0.003, 0.002]
-            },            
-            "locations": {
-                "L1": {
-                    "latitude (deg)": 0.0,
-                    "longitude (deg)": 0.0,
-                    "disposal": {
-                        "P2": {
-                            "cost ($/tonne)": [-10.0, -10.0],
-                            "limit (tonne)": [1.0, 1.0]
-                        },
-                        "P3": {
-                            "cost ($/tonne)": [-10.0, -10.0],
-                            "limit (tonne)": [1.0, 1.0]
-                        }
-                    },
-                    "capacities (tonne)": {
-                        "250.0": {
-                            "opening cost ($)": [500.0, 500.0],
-                            "fixed operating cost ($)": [30.0, 30.0],
-                            "variable operating cost ($/tonne)": [30.0, 30.0]
-                        },
-                        "1000.0": {
-                            "opening cost ($)": [1250.0, 1250.0],
-                            "fixed operating cost ($)": [30.0, 30.0],
-                            "variable operating cost ($/tonne)": [30.0, 30.0]
-                        }
-                    }
-                },
-                "L2": {
-                    "latitude (deg)": 0.5,
-                    "longitude (deg)": 0.5,
-                    "capacities (tonne)": {
-                        "0.0": {
-                            "opening cost ($)": [1000, 1000],
-                            "fixed operating cost ($)": [50.0, 50.0],
-                            "variable operating cost ($/tonne)": [50.0, 50.0]
-                        },
-                        "10000.0": {
-                            "opening cost ($)": [10000, 10000],
-                            "fixed operating cost ($)": [50.0, 50.0],
-                            "variable operating cost ($/tonne)": [50.0, 50.0]
-                        }
-                    }
-                }               
-            }
-        },
-        "F2": {
-            "input": "P2",
-            "outputs (tonne/tonne)": {
-                "P3": 0.05,
-                "P4": 0.80
-            },
-            "locations": {
-                "L3": {
-                    "latitude (deg)": 25.0,
-                    "longitude (deg)": 65.0,
-                    "disposal": {
-                        "P3": {
-                            "cost ($/tonne)": [100.0, 100.0]
-                        }
-                    },
-                    "capacities (tonne)": {
-                        "1000.0": {
-                            "opening cost ($)": [3000, 3000],
-                            "fixed operating cost ($)": [50.0, 50.0],
-                            "variable operating cost ($/tonne)": [50.0, 50.0]
-                        }
-                    }
-                },
-                "L4": {
-                    "latitude (deg)": 0.75,
-                    "longitude (deg)": 0.20,
-                    "capacities (tonne)": {
-                        "10000": {
-                            "opening cost ($)": [3000, 3000],
-                            "fixed operating cost ($)": [50.0, 50.0],
-                            "variable operating cost ($/tonne)": [50.0, 50.0]
-                        }
-                    }
-                }
-            }
-        },
-        "F3": {
-            "input": "P4",
-            "locations": {
-                "L5": {
-                    "latitude (deg)": 100.0,
-                    "longitude (deg)": 100.0,
-                    "capacities (tonne)": {
-                        "15000": {
-                            "opening cost ($)": [0.0, 0.0],
-                            "fixed operating cost ($)": [0.0, 0.0],
-                            "variable operating cost ($/tonne)": [-15.0, -15.0]
-                        }
-                    }
-                }           
-            }
-        },
-        "F4": {
-            "input": "P3",
-            "locations": {
-                "L6": {
-                    "latitude (deg)": 50.0,
-                    "longitude (deg)": 50.0,
-                    "capacities (tonne)": {
-                        "10000": {
-                            "opening cost ($)": [0.0, 0.0],
-                            "fixed operating cost ($)": [0.0, 0.0],
-                            "variable operating cost ($/tonne)": [-15.0, -15.0]
-                        }
-                    }
-                }           
-            }
-        }
-    }
-}
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -1,23 +0,0 @@
-site_name: RELOG
-theme: cinder
-copyright: "Copyright © 2020, UChicago Argonne, LLC. All Rights Reserved."
-repo_url: https://github.com/ANL-CEEESA/RELOG
-edit_uri: edit/master/src/docs/
-nav:
-    - Home: index.md
-    - Usage: usage.md
-    - Data Format: format.md
-    - Reports: reports.md
-    - Optimization Model: model.md
-plugins:
-  - search
-markdown_extensions:
-  - admonition  
-  - mdx_math  
-extra_javascript: 
-    - https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML
-    - js/mathjax.js
-docs_dir: src/docs
-site_dir: docs
-extra_css:
-    - "css/custom.css"
--- a/src/RELOG.jl
+++ b/src/RELOG.jl
@@ -4,20 +4,24 @@

 module RELOG

-include("instance/structs.jl")
+using Pkg

+version() = Pkg.dependencies()[Base.UUID("a2afcdf7-cf04-4913-85f9-c0d81ddf2008")].version
+
+include("instance/structs.jl")
 include("graph/structs.jl")

+include("instance/geodb.jl")
+include("graph/dist.jl")
 include("graph/build.jl")
 include("graph/csv.jl")
 include("instance/compress.jl")
-include("instance/geodb.jl")
 include("instance/parse.jl")
 include("instance/validate.jl")
 include("model/build.jl")
 include("model/getsol.jl")
-include("model/solve.jl")
 include("model/resolve.jl")
+include("model/solve.jl")
 include("reports/plant_emissions.jl")
 include("reports/plant_outputs.jl")
 include("reports/plants.jl")
--- a/src/docs/css/custom.css
+++ b/src/docs/css/custom.css
@@ -1,28 +0,0 @@
-.navbar-default {
-  border-bottom: 0px;
-  background-color: #fff;
-  box-shadow: 0px 0px 15px rgba(0, 0, 0, 0.2);
-}
-
-a, .navbar-default a {
-  color: #06a !important;
-  font-weight: normal;
-}
-
-.disabled > a {
-  color: #999 !important;
-}
-
-.navbar-default a:hover,
-.navbar-default .active,
-.active > a {
-  background-color: #f0f0f0 !important;
-}
-
-.icon-bar {
-  background-color: #666 !important;
-}
-
-.navbar-collapse {
-  border-color: #fff !important;
-}
--- a/src/docs/js/mathjax.js
+++ b/src/docs/js/mathjax.js
@@ -1,8 +0,0 @@
-MathJax.Hub.Config({
-  "tex2jax": { inlineMath: [ [ '$', '$' ] ] }
-});
-MathJax.Hub.Config({
-  config: ["MMLorHTML.js"],
-  jax: ["input/TeX", "output/HTML-CSS", "output/NativeMML"],
-  extensions: ["MathMenu.js", "MathZoom.js"]
-});
--- a/src/graph/build.jl
+++ b/src/graph/build.jl
@@ -2,14 +2,6 @@
 # Copyright (C) 2020, UChicago Argonne, LLC. All rights reserved.
 # Released under the modified BSD license. See COPYING.md for more details.

-using Geodesy
-
-function calculate_distance(source_lat, source_lon, dest_lat, dest_lon)::Float64
-    x = LLA(source_lat, source_lon, 0.0)
-    y = LLA(dest_lat, dest_lon, 0.0)
-    return round(distance(x, y) / 1000.0, digits = 2)
-end
-
 function build_graph(instance::Instance)::Graph
    arcs = []
    next_index = 0
@@ -18,6 +10,7 @@ function build_graph(instance::Instance)::Graph
    collection_shipping_nodes = ShippingNode[]

    name_to_process_node_map = Dict{Tuple{AbstractString,AbstractString},ProcessNode}()
+    collection_center_to_node = Dict()

    process_nodes_by_input_product =
        Dict(product => ProcessNode[] for product in instance.products)
@@ -27,6 +20,7 @@ function build_graph(instance::Instance)::Graph
    for center in instance.collection_centers
        node = ShippingNode(next_index, center, center.product, [], [])
        next_index += 1
+        collection_center_to_node[center] = node
        push!(collection_shipping_nodes, node)
    end

@@ -50,11 +44,12 @@ function build_graph(instance::Instance)::Graph
    # Build arcs from collection centers to plants, and from one plant to another
    for source in [collection_shipping_nodes; plant_shipping_nodes]
        for dest in process_nodes_by_input_product[source.product]
-            distance = calculate_distance(
+            distance = _calculate_distance(
                source.location.latitude,
                source.location.longitude,
                dest.location.latitude,
                dest.location.longitude,
+                instance.distance_metric,
            )
            values = Dict("distance" => distance)
            arc = Arc(source, dest, values)
@@ -83,6 +78,7 @@ function build_graph(instance::Instance)::Graph
        collection_shipping_nodes,
        arcs,
        name_to_process_node_map,
+        collection_center_to_node,
    )
 end

--- a/src/graph/dist.jl
+++ b/src/graph/dist.jl
@@ -0,0 +1,60 @@
+# RELOG: Reverse Logistics Optimization
+# Copyright (C) 2020, UChicago Argonne, LLC. All rights reserved.
+# Released under the modified BSD license. See COPYING.md for more details.
+
+using Geodesy
+using NearestNeighbors
+using DataFrames
+
+function _calculate_distance(
+    source_lat,
+    source_lon,
+    dest_lat,
+    dest_lon,
+    ::EuclideanDistance,
+)::Float64
+    x = LLA(source_lat, source_lon, 0.0)
+    y = LLA(dest_lat, dest_lon, 0.0)
+    return round(euclidean_distance(x, y) / 1000.0, digits = 3)
+end
+
+function _calculate_distance(
+    source_lat,
+    source_lon,
+    dest_lat,
+    dest_lon,
+    metric::KnnDrivingDistance,
+)::Float64
+    if metric.tree === nothing
+        basedir = joinpath(dirname(@__FILE__), "..", "..", "data")
+        csv_filename = joinpath(basedir, "dist_driving.csv")
+
+        # Download pre-computed driving data
+        if !isfile(csv_filename)
+            _download_zip(
+                "https://axavier.org/RELOG/0.6/data/dist_driving_0b9a6ad6.zip",
+                basedir,
+                csv_filename,
+                0x0b9a6ad6,
+            )
+        end
+
+        # Fit kNN model
+        df = DataFrame(CSV.File(csv_filename, missingstring = "NaN"))
+        dropmissing!(df)
+        coords = Matrix(df[!, [:source_lat, :source_lon, :dest_lat, :dest_lon]])'
+        metric.ratios = Matrix(df[!, [:ratio]])
+        metric.tree = KDTree(coords)
+    end
+
+    # Compute Euclidean distance
+    dist_euclidean =
+        _calculate_distance(source_lat, source_lon, dest_lat, dest_lon, EuclideanDistance())
+
+    # Predict ratio
+    idxs, _ = knn(metric.tree, [source_lat, source_lon, dest_lat, dest_lon], 5)
+    ratio_pred = mean(metric.ratios[idxs])
+    dist_pred = round(dist_euclidean * ratio_pred, digits = 3)
+    isfinite(dist_pred) || error("non-finite distance detected: $dist_pred")
+    return dist_pred
+end
--- a/src/graph/structs.jl
+++ b/src/graph/structs.jl
@@ -33,6 +33,7 @@ mutable struct Graph
    collection_shipping_nodes::Vector{ShippingNode}
    arcs::Vector{Arc}
    name_to_process_node_map::Dict{Tuple{AbstractString,AbstractString},ProcessNode}
+    collection_center_to_node::Dict{CollectionCenter,ShippingNode}
 end

 function Base.show(io::IO, instance::Graph)
--- a/src/instance/parse.jl
+++ b/src/instance/parse.jl
@@ -23,8 +23,20 @@ function parse(json)::Instance
    validate(json, Schema(json_schema))

    building_period = [1]
-    if "building period (years)" in keys(json)
-        building_period = json["building period (years)"]
+    if "building period (years)" in keys(json["parameters"])
+        building_period = json["parameters"]["building period (years)"]
+    end
+
+    distance_metric = EuclideanDistance()
+    if "distance metric" in keys(json["parameters"])
+        metric_name = json["parameters"]["distance metric"]
+        if metric_name == "driving"
+            distance_metric = KnnDrivingDistance()
+        elseif metric_name == "Euclidean"
+            # nop
+        else
+            error("Unknown distance metric: $metric_name")
+        end
    end

    plants = Plant[]
@@ -37,6 +49,8 @@ function parse(json)::Instance
        cost = product_dict["transportation cost (\$/km/tonne)"]
        energy = zeros(T)
        emissions = Dict()
+        disposal_limit = zeros(T)
+        disposal_cost = zeros(T)

        if "transportation energy (J/km/tonne)" in keys(product_dict)
            energy = product_dict["transportation energy (J/km/tonne)"]
@@ -46,7 +60,25 @@ function parse(json)::Instance
            emissions = product_dict["transportation emissions (tonne/km/tonne)"]
        end

-        product = Product(product_name, cost, energy, emissions)
+        if "disposal limit (tonne)" in keys(product_dict)
+            disposal_limit = product_dict["disposal limit (tonne)"]
+        end
+
+        if "disposal cost (\$/tonne)" in keys(product_dict)
+            disposal_cost = product_dict["disposal cost (\$/tonne)"]
+        end
+
+        prod_centers = []
+
+        product = Product(
+            product_name,
+            cost,
+            energy,
+            emissions,
+            disposal_limit,
+            disposal_cost,
+            prod_centers,
+        )
        push!(products, product)
        prod_name_to_product[product_name] = product

@@ -66,6 +98,7 @@ function parse(json)::Instance
                    product,
                    center_dict["amount (tonne)"],
                )
+                push!(prod_centers, center)
                push!(collection_centers, center)
            end
        end
@@ -176,5 +209,12 @@ function parse(json)::Instance
    @info @sprintf("%12d collection centers", length(collection_centers))
    @info @sprintf("%12d candidate plant locations", length(plants))

-    return Instance(T, products, collection_centers, plants, building_period)
+    return Instance(
+        T,
+        products,
+        collection_centers,
+        plants,
+        building_period,
+        distance_metric,
+    )
 end
--- a/src/instance/structs.jl
+++ b/src/instance/structs.jl
@@ -13,6 +13,9 @@ mutable struct Product
    transportation_cost::Vector{Float64}
    transportation_energy::Vector{Float64}
    transportation_emissions::Dict{String,Vector{Float64}}
+    disposal_limit::Vector{Float64}
+    disposal_cost::Vector{Float64}
+    collection_centers::Vector
 end

 mutable struct CollectionCenter
@@ -48,10 +51,21 @@ mutable struct Plant
    storage_cost::Vector{Float64}
 end

+
+abstract type DistanceMetric end
+
+Base.@kwdef mutable struct KnnDrivingDistance <: DistanceMetric
+    tree = nothing
+    ratios = nothing
+end
+
+mutable struct EuclideanDistance <: DistanceMetric end
+
 mutable struct Instance
    time::Int64
    products::Vector{Product}
    collection_centers::Vector{CollectionCenter}
    plants::Vector{Plant}
    building_period::Vector{Int64}
+    distance_metric::DistanceMetric
 end
--- a/src/model/build.jl
+++ b/src/model/build.jl
@@ -2,7 +2,7 @@
 # Copyright (C) 2020, UChicago Argonne, LLC. All rights reserved.
 # Released under the modified BSD license. See COPYING.md for more details.

-using JuMP, LinearAlgebra, Geodesy, Cbc, Clp, ProgressBars, Printf, DataStructures
+using JuMP, LinearAlgebra, Geodesy, ProgressBars, Printf, DataStructures

 function build_model(instance::Instance, graph::Graph, optimizer)::JuMP.Model
    model = Model(optimizer)
@@ -20,13 +20,17 @@ function create_vars!(model::JuMP.Model)
    graph, T = model[:graph], model[:instance].time
    model[:flow] =
        Dict((a, t) => @variable(model, lower_bound = 0) for a in graph.arcs, t = 1:T)
-    model[:dispose] = Dict(
+    model[:plant_dispose] = Dict(
        (n, t) => @variable(
            model,
            lower_bound = 0,
            upper_bound = n.location.disposal_limit[n.product][t]
        ) for n in values(graph.plant_shipping_nodes), t = 1:T
    )
+    model[:collection_dispose] = Dict(
+        (n, t) => @variable(model, lower_bound = 0,) for
+        n in values(graph.collection_shipping_nodes), t = 1:T
+    )
    model[:store] = Dict(
        (n, t) =>
            @variable(model, lower_bound = 0, upper_bound = n.location.storage_limit)
@@ -131,14 +135,25 @@ function create_objective_function!(model::JuMP.Model)
        end
    end

-    # Shipping node costs
+    # Plant shipping node costs
    for n in values(graph.plant_shipping_nodes), t = 1:T

        # Disposal costs
        add_to_expression!(
            obj,
            n.location.disposal_cost[n.product][t],
-            model[:dispose][n, t],
+            model[:plant_dispose][n, t],
+        )
+    end
+
+    # Collection shipping node costs
+    for n in values(graph.collection_shipping_nodes), t = 1:T
+
+        # Disposal costs
+        add_to_expression!(
+            obj,
+            n.location.product.disposal_cost[t],
+            model[:collection_dispose][n, t],
        )
    end

@@ -154,16 +169,29 @@ function create_shipping_node_constraints!(model::JuMP.Model)
        for n in graph.collection_shipping_nodes
            model[:eq_balance][n, t] = @constraint(
                model,
-                sum(model[:flow][a, t] for a in n.outgoing_arcs) == n.location.amount[t]
+                sum(model[:flow][a, t] for a in n.outgoing_arcs) ==
+                n.location.amount[t] + model[:collection_dispose][n, t]
            )
        end
+        for prod in model[:instance].products
+            if isempty(prod.collection_centers)
+                continue
+            end
+            expr = AffExpr()
+            for center in prod.collection_centers
+                n = graph.collection_center_to_node[center]
+                add_to_expression!(expr, model[:collection_dispose][n, t])
+            end
+            @constraint(model, expr <= prod.disposal_limit[t])
+        end

        # Plants
        for n in graph.plant_shipping_nodes
            @constraint(
                model,
                sum(model[:flow][a, t] for a in n.incoming_arcs) ==
-                sum(model[:flow][a, t] for a in n.outgoing_arcs) + model[:dispose][n, t]
+                sum(model[:flow][a, t] for a in n.outgoing_arcs) +
+                model[:plant_dispose][n, t]
            )
        end
    end
--- a/src/model/getsol.jl
+++ b/src/model/getsol.jl
@@ -2,7 +2,7 @@
 # Copyright (C) 2020, UChicago Argonne, LLC. All rights reserved.
 # Released under the modified BSD license. See COPYING.md for more details.

-using JuMP, LinearAlgebra, Geodesy, Cbc, Clp, ProgressBars, Printf, DataStructures
+using JuMP, LinearAlgebra, Geodesy, ProgressBars, Printf, DataStructures

 function get_solution(model::JuMP.Model; marginal_costs = true)
    graph, instance = model[:graph], model[:instance]
@@ -39,21 +39,24 @@ function get_solution(model::JuMP.Model; marginal_costs = true)
    end

    # Products
-    if marginal_costs
-        for n in graph.collection_shipping_nodes
-            location_dict = OrderedDict{Any,Any}(
-                "Marginal cost (\$/tonne)" => [
-                    round(abs(JuMP.shadow_price(model[:eq_balance][n, t])), digits = 2) for t = 1:T
-                ],
-                "Latitude (deg)" => n.location.latitude,
-                "Longitude (deg)" => n.location.longitude,
-                "Amount (tonne)" => n.location.amount,
-            )
-            if n.product.name ∉ keys(output["Products"])
-                output["Products"][n.product.name] = OrderedDict()
-            end
-            output["Products"][n.product.name][n.location.name] = location_dict
+    for n in graph.collection_shipping_nodes
+        location_dict = OrderedDict{Any,Any}(
+            "Latitude (deg)" => n.location.latitude,
+            "Longitude (deg)" => n.location.longitude,
+            "Amount (tonne)" => n.location.amount,
+            "Dispose (tonne)" =>
+                [JuMP.value(model[:collection_dispose][n, t]) for t = 1:T],
+        )
+        if marginal_costs
+            location_dict["Marginal cost (\$/tonne)"] = [
+                round(abs(JuMP.shadow_price(model[:eq_balance][n, t])), digits = 2) for
+                t = 1:T
+            ]
        end
+        if n.product.name ∉ keys(output["Products"])
+            output["Products"][n.product.name] = OrderedDict()
+        end
+        output["Products"][n.product.name][n.location.name] = location_dict
    end

    # Plants
@@ -178,13 +181,14 @@ function get_solution(model::JuMP.Model; marginal_costs = true)
            plant_dict["Total output"][product_name] = zeros(T)
            plant_dict["Output"]["Send"][product_name] = product_dict = OrderedDict()

-            disposal_amount = [JuMP.value(model[:dispose][shipping_node, t]) for t = 1:T]
+            disposal_amount =
+                [JuMP.value(model[:plant_dispose][shipping_node, t]) for t = 1:T]
            if sum(disposal_amount) > 1e-5
                skip_plant = false
                plant_dict["Output"]["Dispose"][product_name] =
                    disposal_dict = OrderedDict()
                disposal_dict["Amount (tonne)"] =
-                    [JuMP.value(model[:dispose][shipping_node, t]) for t = 1:T]
+                    [JuMP.value(model[:plant_dispose][shipping_node, t]) for t = 1:T]
                disposal_dict["Cost (\$)"] = [
                    disposal_dict["Amount (tonne)"][t] *
                    plant.disposal_cost[shipping_node.product][t] for t = 1:T
--- a/src/model/solve.jl
+++ b/src/model/solve.jl
@@ -2,26 +2,26 @@
 # Copyright (C) 2020, UChicago Argonne, LLC. All rights reserved.
 # Released under the modified BSD license. See COPYING.md for more details.

-using JuMP, LinearAlgebra, Geodesy, Cbc, Clp, ProgressBars, Printf, DataStructures
+using JuMP, LinearAlgebra, Geodesy, ProgressBars, Printf, DataStructures, HiGHS

 function _get_default_milp_optimizer()
-    return optimizer_with_attributes(Cbc.Optimizer, "logLevel" => 0)
+    return optimizer_with_attributes(HiGHS.Optimizer)
 end

 function _get_default_lp_optimizer()
-    return optimizer_with_attributes(Clp.Optimizer, "LogLevel" => 0)
+    return optimizer_with_attributes(HiGHS.Optimizer)
 end


 function _print_graph_stats(instance::Instance, graph::Graph)::Nothing
-    @info @sprintf("    %12d time periods", instance.time)
-    @info @sprintf("    %12d process nodes", length(graph.process_nodes))
-    @info @sprintf("    %12d shipping nodes (plant)", length(graph.plant_shipping_nodes))
+    @info @sprintf("%12d time periods", instance.time)
+    @info @sprintf("%12d process nodes", length(graph.process_nodes))
+    @info @sprintf("%12d shipping nodes (plant)", length(graph.plant_shipping_nodes))
    @info @sprintf(
-        "    %12d shipping nodes (collection)",
+        "%12d shipping nodes (collection)",
        length(graph.collection_shipping_nodes)
    )
-    @info @sprintf("    %12d arcs", length(graph.arcs))
+    @info @sprintf("%12d arcs", length(graph.arcs))
    return
 end

@@ -41,7 +41,7 @@ function solve(
        else
            # If only MIP optimizer is provided, use it as
            # LP solver too.
-            lp_optimizer = optimizer 
+            lp_optimizer = optimizer
        end
    end

@@ -98,7 +98,13 @@ function solve(filename::AbstractString; heuristic = false, kwargs...)
    if heuristic && instance.time > 1
        @info "Solving single-period version..."
        compressed = _compress(instance)
-        csol = solve(compressed; output = nothing, marginal_costs = false, kwargs...)
+        csol, _ = solve(
+            compressed;
+            return_model = true,
+            output = nothing,
+            marginal_costs = false,
+            kwargs...,
+        )
        @info "Filtering candidate locations..."
        selected_pairs = []
        for (plant_name, plant_dict) in csol["Plants"]
--- a/src/reports/products.jl
+++ b/src/reports/products.jl
@@ -13,6 +13,7 @@ function products_report(solution; marginal_costs = true)::DataFrame
    df."longitude (deg)" = Float64[]
    df."year" = Int[]
    df."amount (tonne)" = Float64[]
+    df."amount disposed (tonne)" = Float64[]
    df."marginal cost (\$/tonne)" = Float64[]
    T = length(solution["Energy"]["Plants (GJ)"])
    for (prod_name, prod_dict) in solution["Products"]
@@ -22,6 +23,7 @@ function products_report(solution; marginal_costs = true)::DataFrame
                latitude = round(location_dict["Latitude (deg)"], digits = 6)
                longitude = round(location_dict["Longitude (deg)"], digits = 6)
                amount = location_dict["Amount (tonne)"][year]
+                amount_disposed = location_dict["Dispose (tonne)"][year]
                push!(
                    df,
                    [
@@ -32,6 +34,7 @@ function products_report(solution; marginal_costs = true)::DataFrame
                        year,
                        amount,
                        marginal_cost,
+                        amount_disposed,
                    ],
                )
            end
--- a/src/schemas/input.json
+++ b/src/schemas/input.json
@@ -14,6 +14,9 @@
            "properties": {
                "time horizon (years)": {
                    "type": "number"
+                },
+                "distance metric": {
+                    "type": "string"
                }
            },
            "required": [
@@ -169,6 +172,12 @@
                    },
                    "initial amounts": {
                        "$ref": "#/definitions/InitialAmount"
+                    },
+                    "disposal limit (tonne)": {
+                        "$ref": "#/definitions/TimeSeries"
+                    },
+                    "disposal cost ($/tonne)": {
+                        "$ref": "#/definitions/TimeSeries"
                    }
                },
                "required": [
--- a/src/sysimage.jl
+++ b/src/sysimage.jl
@@ -1,15 +0,0 @@
-using PackageCompiler
-
-using Cbc
-using Clp
-using Geodesy
-using JSON
-using JSONSchema
-using JuMP
-using MathOptInterface
-using ProgressBars
-
-pkg = [:Cbc, :Clp, :Geodesy, :JSON, :JSONSchema, :JuMP, :MathOptInterface, :ProgressBars]
-
-@info "Building system image..."
-create_sysimage(pkg, sysimage_path = "build/sysimage.so")
--- a/src/web/run.jl
+++ b/src/web/run.jl
@@ -1,40 +1,34 @@
 println("Initializing...")

 using Logging
-using Cbc
-using Clp
 using JSON
 using JuMP
+using HiGHS
 using RELOG

 function solve(root, filename)
    ref_file = "$root/$filename"
    optimizer = optimizer_with_attributes(
-        Cbc.Optimizer,
-        "seconds" => 900,
+        HiGHS.Optimizer,
+        "time_limit" => parse(Float64, ENV["RELOG_TIME_LIMIT_SEC"]),
    )
    ref_solution, ref_model = RELOG.solve(
        ref_file,
-        optimizer=optimizer,
-        lp_optimizer=Clp.Optimizer,
-        return_model=true,
-        marginal_costs=true,
+        heuristic = true,
+        optimizer = optimizer,
+        lp_optimizer = HiGHS.Optimizer,
+        return_model = true,
+        marginal_costs = true,
    )
    Libc.flush_cstdio()
    flush(stdout)
    sleep(1)
-    
+
    if length(ref_solution) == 0
        return
    end
-    RELOG.write_products_report(
-        ref_solution,
-        replace(ref_file, ".json" => "_products.csv"),
-    )
-    RELOG.write_plants_report(
-        ref_solution,
-        replace(ref_file, ".json" => "_plants.csv"),
-    )
+    RELOG.write_products_report(ref_solution, replace(ref_file, ".json" => "_products.csv"))
+    RELOG.write_plants_report(ref_solution, replace(ref_file, ".json" => "_plants.csv"))
    RELOG.write_plant_outputs_report(
        ref_solution,
        replace(ref_file, ".json" => "_plant_outputs.csv"),
@@ -43,10 +37,7 @@ function solve(root, filename)
        ref_solution,
        replace(ref_file, ".json" => "_plant_emissions.csv"),
    )
-    RELOG.write_transportation_report(
-        ref_solution,
-        replace(ref_file, ".json" => "_tr.csv"),
-    )
+    RELOG.write_transportation_report(ref_solution, replace(ref_file, ".json" => "_tr.csv"))
    RELOG.write_transportation_emissions_report(
        ref_solution,
        replace(ref_file, ".json" => "_tr_emissions.csv"),
@@ -60,16 +51,13 @@ function solve(root, filename)
        sc_solution = RELOG.resolve(
            ref_model,
            scenario,
-            optimizer=optimizer,
-            lp_optimizer=Clp.Optimizer,
+            optimizer = optimizer,
+            lp_optimizer = HiGHS.Optimizer,
        )
        if length(sc_solution) == 0
            return
        end
-        RELOG.write_plants_report(
-            sc_solution,
-            replace(scenario, ".json" => "_plants.csv"),
-        )
+        RELOG.write_plants_report(sc_solution, replace(scenario, ".json" => "_plants.csv"))
        RELOG.write_products_report(
            sc_solution,
            replace(scenario, ".json" => "_products.csv"),
@@ -114,10 +102,7 @@ function solve_recursive(path)
            endswith(filename, "_plants.csv") || continue
            push!(
                results,
-                joinpath(
-                    replace(root, path => ""),
-                    replace(filename, "_plants.csv" => ""),
-                ),
+                joinpath(replace(root, path => ""), replace(filename, "_plants.csv" => "")),
            )
        end
    end
@@ -128,4 +113,4 @@ function solve_recursive(path)
    run(`zip -r output.zip .`)
 end

-solve_recursive(ARGS[1])
+solve_recursive(ARGS[1])
--- a/src/web/web.jl
+++ b/src/web/web.jl
@@ -32,11 +32,11 @@ function submit(req::HTTP.Request)
    end

    # Run job
-    run(`bash -c "(julia --project=$PROJECT_DIR $PROJECT_DIR/src/web/run.jl $job_path 2>&1 | tee $job_path/solve.log) >/dev/null 2>&1 &"`)
-
-    response = Dict(
-        "job_id" => job_id,
+    run(
+        `bash -c "(julia --project=$PROJECT_DIR $PROJECT_DIR/src/web/run.jl $job_path 2>&1 | tee $job_path/solve.log) >/dev/null 2>&1 &"`,
    )
+
+    response = Dict("job_id" => job_id)
    return HTTP.Response(200, body = JSON.json(response))
 end

@@ -63,4 +63,3 @@ function web(host = "127.0.0.1", port = 8080)
    HTTP.serve(ROUTER, host, port)
    Base.exit_on_sigint(true)
 end
-
--- a/test/Project.toml
+++ b/test/Project.toml
@@ -0,0 +1,19 @@
+name = "RELOGT"
+uuid = "a6dae211-05d8-42ed-9081-b88c982fc90a"
+authors = ["Alinson S. Xavier <git@axavier.org>"]
+version = "0.1.0"
+
+[deps]
+Cbc = "9961bab8-2fa3-5c5a-9d89-47fab24efd76"
+GZip = "92fee26a-97fe-5a0c-ad85-20a5f3185b63"
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+JuMP = "4076af6c-e467-56ae-b986-b466b2749572"
+JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
+MathOptInterface = "b8f27783-ece8-5eb3-8dc8-9495eed66fee"
+Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+RELOG = "a2afcdf7-cf04-4913-85f9-c0d81ddf2008"
+Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[compat]
+JuliaFormatter = "1"
--- a/test/fixtures/s1.json
+++ b/test/fixtures/s1.json
@@ -0,0 +1,358 @@
+{
+    "parameters": {
+        "time horizon (years)": 2,
+        "distance metric": "driving"
+    },
+    "products": {
+        "P1": {
+            "transportation cost ($/km/tonne)": [
+                0.015,
+                0.015
+            ],
+            "transportation energy (J/km/tonne)": [
+                0.12,
+                0.11
+            ],
+            "transportation emissions (tonne/km/tonne)": {
+                "CO2": [
+                    0.052,
+                    0.050
+                ],
+                "CH4": [
+                    0.003,
+                    0.002
+                ]
+            },
+            "initial amounts": {
+                "C1": {
+                    "latitude (deg)": 7.0,
+                    "longitude (deg)": 7.0,
+                    "amount (tonne)": [
+                        934.56,
+                        934.56
+                    ]
+                },
+                "C2": {
+                    "latitude (deg)": 7.0,
+                    "longitude (deg)": 19.0,
+                    "amount (tonne)": [
+                        198.95,
+                        198.95
+                    ]
+                },
+                "C3": {
+                    "latitude (deg)": 84.0,
+                    "longitude (deg)": 76.0,
+                    "amount (tonne)": [
+                        212.97,
+                        212.97
+                    ]
+                },
+                "C4": {
+                    "latitude (deg)": 21.0,
+                    "longitude (deg)": 16.0,
+                    "amount (tonne)": [
+                        352.19,
+                        352.19
+                    ]
+                },
+                "C5": {
+                    "latitude (deg)": 32.0,
+                    "longitude (deg)": 92.0,
+                    "amount (tonne)": [
+                        510.33,
+                        510.33
+                    ]
+                },
+                "C6": {
+                    "latitude (deg)": 14.0,
+                    "longitude (deg)": 62.0,
+                    "amount (tonne)": [
+                        471.66,
+                        471.66
+                    ]
+                },
+                "C7": {
+                    "latitude (deg)": 30.0,
+                    "longitude (deg)": 83.0,
+                    "amount (tonne)": [
+                        785.21,
+                        785.21
+                    ]
+                },
+                "C8": {
+                    "latitude (deg)": 35.0,
+                    "longitude (deg)": 40.0,
+                    "amount (tonne)": [
+                        706.17,
+                        706.17
+                    ]
+                },
+                "C9": {
+                    "latitude (deg)": 74.0,
+                    "longitude (deg)": 52.0,
+                    "amount (tonne)": [
+                        30.08,
+                        30.08
+                    ]
+                },
+                "C10": {
+                    "latitude (deg)": 22.0,
+                    "longitude (deg)": 54.0,
+                    "amount (tonne)": [
+                        536.52,
+                        536.52
+                    ]
+                }
+            },
+            "disposal limit (tonne)": [
+                1.0,
+                1.0
+            ],
+            "disposal cost ($/tonne)": [
+                -1000,
+                -1000
+            ]
+        },
+        "P2": {
+            "transportation cost ($/km/tonne)": [
+                0.02,
+                0.02
+            ]
+        },
+        "P3": {
+            "transportation cost ($/km/tonne)": [
+                0.0125,
+                0.0125
+            ]
+        },
+        "P4": {
+            "transportation cost ($/km/tonne)": [
+                0.0175,
+                0.0175
+            ]
+        }
+    },
+    "plants": {
+        "F1": {
+            "input": "P1",
+            "outputs (tonne/tonne)": {
+                "P2": 0.2,
+                "P3": 0.5
+            },
+            "energy (GJ/tonne)": [
+                0.12,
+                0.11
+            ],
+            "emissions (tonne/tonne)": {
+                "CO2": [
+                    0.052,
+                    0.050
+                ],
+                "CH4": [
+                    0.003,
+                    0.002
+                ]
+            },
+            "locations": {
+                "L1": {
+                    "latitude (deg)": 0.0,
+                    "longitude (deg)": 0.0,
+                    "disposal": {
+                        "P2": {
+                            "cost ($/tonne)": [
+                                -10.0,
+                                -10.0
+                            ],
+                            "limit (tonne)": [
+                                1.0,
+                                1.0
+                            ]
+                        },
+                        "P3": {
+                            "cost ($/tonne)": [
+                                -10.0,
+                                -10.0
+                            ],
+                            "limit (tonne)": [
+                                1.0,
+                                1.0
+                            ]
+                        }
+                    },
+                    "capacities (tonne)": {
+                        "250.0": {
+                            "opening cost ($)": [
+                                500.0,
+                                500.0
+                            ],
+                            "fixed operating cost ($)": [
+                                30.0,
+                                30.0
+                            ],
+                            "variable operating cost ($/tonne)": [
+                                30.0,
+                                30.0
+                            ]
+                        },
+                        "1000.0": {
+                            "opening cost ($)": [
+                                1250.0,
+                                1250.0
+                            ],
+                            "fixed operating cost ($)": [
+                                30.0,
+                                30.0
+                            ],
+                            "variable operating cost ($/tonne)": [
+                                30.0,
+                                30.0
+                            ]
+                        }
+                    }
+                },
+                "L2": {
+                    "latitude (deg)": 0.5,
+                    "longitude (deg)": 0.5,
+                    "capacities (tonne)": {
+                        "0.0": {
+                            "opening cost ($)": [
+                                1000,
+                                1000
+                            ],
+                            "fixed operating cost ($)": [
+                                50.0,
+                                50.0
+                            ],
+                            "variable operating cost ($/tonne)": [
+                                50.0,
+                                50.0
+                            ]
+                        },
+                        "10000.0": {
+                            "opening cost ($)": [
+                                10000,
+                                10000
+                            ],
+                            "fixed operating cost ($)": [
+                                50.0,
+                                50.0
+                            ],
+                            "variable operating cost ($/tonne)": [
+                                50.0,
+                                50.0
+                            ]
+                        }
+                    }
+                }
+            }
+        },
+        "F2": {
+            "input": "P2",
+            "outputs (tonne/tonne)": {
+                "P3": 0.05,
+                "P4": 0.80
+            },
+            "locations": {
+                "L3": {
+                    "latitude (deg)": 25.0,
+                    "longitude (deg)": 65.0,
+                    "disposal": {
+                        "P3": {
+                            "cost ($/tonne)": [
+                                100.0,
+                                100.0
+                            ]
+                        }
+                    },
+                    "capacities (tonne)": {
+                        "1000.0": {
+                            "opening cost ($)": [
+                                3000,
+                                3000
+                            ],
+                            "fixed operating cost ($)": [
+                                50.0,
+                                50.0
+                            ],
+                            "variable operating cost ($/tonne)": [
+                                50.0,
+                                50.0
+                            ]
+                        }
+                    }
+                },
+                "L4": {
+                    "latitude (deg)": 0.75,
+                    "longitude (deg)": 0.20,
+                    "capacities (tonne)": {
+                        "10000": {
+                            "opening cost ($)": [
+                                3000,
+                                3000
+                            ],
+                            "fixed operating cost ($)": [
+                                50.0,
+                                50.0
+                            ],
+                            "variable operating cost ($/tonne)": [
+                                50.0,
+                                50.0
+                            ]
+                        }
+                    }
+                }
+            }
+        },
+        "F3": {
+            "input": "P4",
+            "locations": {
+                "L5": {
+                    "latitude (deg)": 100.0,
+                    "longitude (deg)": 100.0,
+                    "capacities (tonne)": {
+                        "15000": {
+                            "opening cost ($)": [
+                                0.0,
+                                0.0
+                            ],
+                            "fixed operating cost ($)": [
+                                0.0,
+                                0.0
+                            ],
+                            "variable operating cost ($/tonne)": [
+                                -15.0,
+                                -15.0
+                            ]
+                        }
+                    }
+                }
+            }
+        },
+        "F4": {
+            "input": "P3",
+            "locations": {
+                "L6": {
+                    "latitude (deg)": 50.0,
+                    "longitude (deg)": 50.0,
+                    "capacities (tonne)": {
+                        "10000": {
+                            "opening cost ($)": [
+                                0.0,
+                                0.0
+                            ],
+                            "fixed operating cost ($)": [
+                                0.0,
+                                0.0
+                            ],
+                            "variable operating cost ($/tonne)": [
+                                -15.0,
+                                -15.0
+                            ]
+                        }
+                    }
+                }
+            }
+        }
+    }
+}
--- a/test/fixtures/s1.zip
+++ b/test/fixtures/s1.zip
--- a/test/fixtures/s2.json
+++ b/test/fixtures/s2.json
--- a/test/fixtures/solutions/s1.json
+++ b/test/fixtures/solutions/s1.json
--- a/test/fixtures/solutions/s1.log
+++ b/test/fixtures/solutions/s1.log
--- a/test/graph/build_test.jl
+++ b/test/graph/build_test.jl
@@ -1,39 +0,0 @@
-# Copyright (C) 2020 Argonne National Laboratory
-# Written by Alinson Santos Xavier <axavier@anl.gov>
-
-using RELOG
-
-@testset "build_graph" begin
-    basedir = dirname(@__FILE__)
-    instance = RELOG.parsefile("$basedir/../../instances/s1.json")
-    graph = RELOG.build_graph(instance)
-    process_node_by_location_name =
-        Dict(n.location.location_name => n for n in graph.process_nodes)
-
-    @test length(graph.plant_shipping_nodes) == 8
-    @test length(graph.collection_shipping_nodes) == 10
-    @test length(graph.process_nodes) == 6
-
-    node = graph.collection_shipping_nodes[1]
-    @test node.location.name == "C1"
-    @test length(node.incoming_arcs) == 0
-    @test length(node.outgoing_arcs) == 2
-    @test node.outgoing_arcs[1].source.location.name == "C1"
-    @test node.outgoing_arcs[1].dest.location.plant_name == "F1"
-    @test node.outgoing_arcs[1].dest.location.location_name == "L1"
-    @test node.outgoing_arcs[1].values["distance"] == 1095.62
-
-    node = process_node_by_location_name["L1"]
-    @test node.location.plant_name == "F1"
-    @test node.location.location_name == "L1"
-    @test length(node.incoming_arcs) == 10
-    @test length(node.outgoing_arcs) == 2
-
-    node = process_node_by_location_name["L3"]
-    @test node.location.plant_name == "F2"
-    @test node.location.location_name == "L3"
-    @test length(node.incoming_arcs) == 2
-    @test length(node.outgoing_arcs) == 2
-
-    @test length(graph.arcs) == 38
-end
--- a/test/instance/compress_test.jl
+++ b/test/instance/compress_test.jl
@@ -1,53 +0,0 @@
-# Copyright (C) 2020 Argonne National Laboratory
-# Written by Alinson Santos Xavier <axavier@anl.gov>
-
-using RELOG
-
-@testset "compress" begin
-    basedir = dirname(@__FILE__)
-    instance = RELOG.parsefile("$basedir/../../instances/s1.json")
-    compressed = RELOG._compress(instance)
-
-    product_name_to_product = Dict(p.name => p for p in compressed.products)
-    location_name_to_facility = Dict()
-    for p in compressed.plants
-        location_name_to_facility[p.location_name] = p
-    end
-    for c in compressed.collection_centers
-        location_name_to_facility[c.name] = c
-    end
-
-    p1 = product_name_to_product["P1"]
-    p2 = product_name_to_product["P2"]
-    p3 = product_name_to_product["P3"]
-    c1 = location_name_to_facility["C1"]
-    l1 = location_name_to_facility["L1"]
-
-    @test compressed.time == 1
-    @test compressed.building_period == [1]
-
-    @test p1.name == "P1"
-    @test p1.transportation_cost ≈ [0.015]
-    @test p1.transportation_energy ≈ [0.115]
-    @test p1.transportation_emissions["CO2"] ≈ [0.051]
-    @test p1.transportation_emissions["CH4"] ≈ [0.0025]
-
-    @test c1.name == "C1"
-    @test c1.amount ≈ [1869.12]
-
-    @test l1.plant_name == "F1"
-    @test l1.location_name == "L1"
-    @test l1.energy ≈ [0.115]
-    @test l1.emissions["CO2"] ≈ [0.051]
-    @test l1.emissions["CH4"] ≈ [0.0025]
-    @test l1.sizes[1].opening_cost ≈ [500]
-    @test l1.sizes[2].opening_cost ≈ [1250]
-    @test l1.sizes[1].fixed_operating_cost ≈ [60]
-    @test l1.sizes[2].fixed_operating_cost ≈ [60]
-    @test l1.sizes[1].variable_operating_cost ≈ [30]
-    @test l1.sizes[2].variable_operating_cost ≈ [30]
-    @test l1.disposal_limit[p2] ≈ [2.0]
-    @test l1.disposal_limit[p3] ≈ [2.0]
-    @test l1.disposal_cost[p2] ≈ [-10.0]
-    @test l1.disposal_cost[p3] ≈ [-10.0]
-end
--- a/test/instance/geodb_test.jl
+++ b/test/instance/geodb_test.jl
@@ -1,25 +0,0 @@
-# RELOG: Reverse Logistics Optimization
-# Copyright (C) 2020, UChicago Argonne, LLC. All rights reserved.
-# Released under the modified BSD license. See COPYING.md for more details.
-
-using RELOG
-
-@testset "geodb_query (2018-us-county)" begin
-    region = RELOG.geodb_query("2018-us-county:17043")
-    @test region.centroid.lat == 41.83956
-    @test region.centroid.lon == -88.08857
-    @test region.population == 922_921
-end
-
-# @testset "geodb_query (2018-us-zcta)" begin
-#     region = RELOG.geodb_query("2018-us-zcta:60439")
-#     @test region.centroid.lat == 41.68241
-#     @test region.centroid.lon == -87.98954
-# end
-
-@testset "geodb_query (us-state)" begin
-    region = RELOG.geodb_query("us-state:IL")
-    @test region.centroid.lat == 39.73939
-    @test region.centroid.lon == -89.50414
-    @test region.population == 12_671_821
-end
--- a/test/instance/parse_test.jl
+++ b/test/instance/parse_test.jl
@@ -1,86 +0,0 @@
-# Copyright (C) 2020 Argonne National Laboratory
-# Written by Alinson Santos Xavier <axavier@anl.gov>
-
-using RELOG
-
-@testset "parse" begin
-    basedir = dirname(@__FILE__)
-    instance = RELOG.parsefile("$basedir/../../instances/s1.json")
-
-    centers = instance.collection_centers
-    plants = instance.plants
-    products = instance.products
-    location_name_to_plant = Dict(p.location_name => p for p in plants)
-    product_name_to_product = Dict(p.name => p for p in products)
-
-    @test length(centers) == 10
-    @test centers[1].name == "C1"
-    @test centers[1].latitude == 7
-    @test centers[1].latitude == 7
-    @test centers[1].longitude == 7
-    @test centers[1].amount == [934.56, 934.56]
-    @test centers[1].product.name == "P1"
-
-    @test length(plants) == 6
-
-    plant = location_name_to_plant["L1"]
-    @test plant.plant_name == "F1"
-    @test plant.location_name == "L1"
-    @test plant.input.name == "P1"
-    @test plant.latitude == 0
-    @test plant.longitude == 0
-
-    @test length(plant.sizes) == 2
-    @test plant.sizes[1].capacity == 250
-    @test plant.sizes[1].opening_cost == [500, 500]
-    @test plant.sizes[1].fixed_operating_cost == [30, 30]
-    @test plant.sizes[1].variable_operating_cost == [30, 30]
-    @test plant.sizes[2].capacity == 1000
-    @test plant.sizes[2].opening_cost == [1250, 1250]
-    @test plant.sizes[2].fixed_operating_cost == [30, 30]
-    @test plant.sizes[2].variable_operating_cost == [30, 30]
-
-    p2 = product_name_to_product["P2"]
-    p3 = product_name_to_product["P3"]
-    @test length(plant.output) == 2
-    @test plant.output[p2] == 0.2
-    @test plant.output[p3] == 0.5
-    @test plant.disposal_limit[p2] == [1, 1]
-    @test plant.disposal_limit[p3] == [1, 1]
-    @test plant.disposal_cost[p2] == [-10, -10]
-    @test plant.disposal_cost[p3] == [-10, -10]
-
-    plant = location_name_to_plant["L3"]
-    @test plant.location_name == "L3"
-    @test plant.input.name == "P2"
-    @test plant.latitude == 25
-    @test plant.longitude == 65
-
-    @test length(plant.sizes) == 2
-    @test plant.sizes[1].capacity == 1000.0
-    @test plant.sizes[1].opening_cost == [3000, 3000]
-    @test plant.sizes[1].fixed_operating_cost == [50, 50]
-    @test plant.sizes[1].variable_operating_cost == [50, 50]
-    @test plant.sizes[1] == plant.sizes[2]
-
-    p4 = product_name_to_product["P4"]
-    @test plant.output[p3] == 0.05
-    @test plant.output[p4] == 0.8
-    @test plant.disposal_limit[p3] == [1e8, 1e8]
-    @test plant.disposal_limit[p4] == [0, 0]
-end
-
-@testset "parse (geodb)" begin
-    basedir = dirname(@__FILE__)
-    instance = RELOG.parsefile("$basedir/../../instances/s2.json")
-
-    centers = instance.collection_centers
-    @test centers[1].name == "C1"
-    @test centers[1].latitude == 41.83956
-    @test centers[1].longitude == -88.08857
-end
-
-# @testset "parse (invalid)" begin
-#     basedir = dirname(@__FILE__)
-#     @test_throws ErrorException RELOG.parsefile("$basedir/../fixtures/s1-wrong-length.json")
-# end
--- a/test/model/build_test.jl
+++ b/test/model/build_test.jl
@@ -1,38 +0,0 @@
-# Copyright (C) 2020 Argonne National Laboratory
-# Written by Alinson Santos Xavier <axavier@anl.gov>
-
-using RELOG, Cbc, JuMP, Printf, JSON, MathOptInterface.FileFormats
-
-@testset "build" begin
-    basedir = dirname(@__FILE__)
-    instance = RELOG.parsefile("$basedir/../../instances/s1.json")
-    graph = RELOG.build_graph(instance)
-    model = RELOG.build_model(instance, graph, Cbc.Optimizer)
-    set_optimizer_attribute(model, "logLevel", 0)
-
-    process_node_by_location_name =
-        Dict(n.location.location_name => n for n in graph.process_nodes)
-
-    shipping_node_by_loc_and_prod_names = Dict(
-        (n.location.location_name, n.product.name) => n for n in graph.plant_shipping_nodes
-    )
-
-    @test length(model[:flow]) == 76
-    @test length(model[:dispose]) == 16
-    @test length(model[:open_plant]) == 12
-    @test length(model[:capacity]) == 12
-    @test length(model[:expansion]) == 12
-
-    l1 = process_node_by_location_name["L1"]
-    v = model[:capacity][l1, 1]
-    @test lower_bound(v) == 0.0
-    @test upper_bound(v) == 1000.0
-
-    v = model[:expansion][l1, 1]
-    @test lower_bound(v) == 0.0
-    @test upper_bound(v) == 750.0
-
-    v = model[:dispose][shipping_node_by_loc_and_prod_names["L1", "P2"], 1]
-    @test lower_bound(v) == 0.0
-    @test upper_bound(v) == 1.0
-end
--- a/test/model/resolve_test.jl
+++ b/test/model/resolve_test.jl
@@ -1,13 +0,0 @@
-# Copyright (C) 2020 Argonne National Laboratory
-# Written by Alinson Santos Xavier <axavier@anl.gov>
-
-using RELOG
-
-BASEDIR = dirname(@__FILE__)
-
-@testset "Resolve" begin
-    # Shoud not crash
-    filename = joinpath(BASEDIR, "..", "..", "instances", "s1.json")
-    solution_old, model_old = RELOG.solve(filename, return_model = true)
-    solution_new = RELOG.resolve(model_old, filename)
-end
--- a/test/model/solve_test.jl
+++ b/test/model/solve_test.jl
@@ -1,61 +0,0 @@
-# Copyright (C) 2020 Argonne National Laboratory
-# Written by Alinson Santos Xavier <axavier@anl.gov>
-
-using RELOG, Cbc, JuMP, Printf, JSON, MathOptInterface.FileFormats
-
-basedir = dirname(@__FILE__)
-
-@testset "solve (exact)" begin
-    solution_filename_a = tempname()
-    solution_filename_b = tempname()
-    solution = RELOG.solve("$basedir/../../instances/s1.json", output = solution_filename_a)
-
-    @test isfile(solution_filename_a)
-
-    RELOG.write(solution, solution_filename_b)
-    @test isfile(solution_filename_b)
-
-    @test "Costs" in keys(solution)
-    @test "Fixed operating (\$)" in keys(solution["Costs"])
-    @test "Transportation (\$)" in keys(solution["Costs"])
-    @test "Variable operating (\$)" in keys(solution["Costs"])
-    @test "Total (\$)" in keys(solution["Costs"])
-
-    @test "Plants" in keys(solution)
-    @test "F1" in keys(solution["Plants"])
-    @test "F2" in keys(solution["Plants"])
-    @test "F3" in keys(solution["Plants"])
-    @test "F4" in keys(solution["Plants"])
-end
-
-@testset "solve (heuristic)" begin
-    # Should not crash
-    solution = RELOG.solve("$basedir/../../instances/s1.json", heuristic = true)
-end
-
-@testset "solve (infeasible)" begin
-    json = JSON.parsefile("$basedir/../../instances/s1.json")
-    for (location_name, location_dict) in json["products"]["P1"]["initial amounts"]
-        location_dict["amount (tonne)"] *= 1000
-    end
-    @test_throws ErrorException("No solution available") RELOG.solve(RELOG.parse(json))
-end
-
-@testset "solve (with storage)" begin
-    basedir = dirname(@__FILE__)
-    filename = "$basedir/../fixtures/storage.json"
-    instance = RELOG.parsefile(filename)
-    @test instance.plants[1].storage_limit == 50.0
-    @test instance.plants[1].storage_cost == [2.0, 1.5, 1.0]
-
-    solution = RELOG.solve(filename)
-    plant_dict = solution["Plants"]["mega plant"]["Chicago"]
-    @test plant_dict["Variable operating cost (\$)"] == [500.0, 0.0, 100.0]
-    @test plant_dict["Process (tonne)"] == [50.0, 0.0, 50.0]
-    @test plant_dict["Storage (tonne)"] == [50.0, 50.0, 0.0]
-    @test plant_dict["Storage cost (\$)"] == [100.0, 75.0, 0.0]
-
-    @test solution["Costs"]["Variable operating (\$)"] == [500.0, 0.0, 100.0]
-    @test solution["Costs"]["Storage (\$)"] == [100.0, 75.0, 0.0]
-    @test solution["Costs"]["Total (\$)"] == [600.0, 75.0, 100.0]
-end
--- a/test/reports_test.jl
+++ b/test/reports_test.jl
@@ -1,21 +0,0 @@
-# RELOG: Reverse Logistics Optimization
-# Copyright (C) 2020, UChicago Argonne, LLC. All rights reserved.
-# Released under the modified BSD license. See COPYING.md for more details.
-
-using RELOG, JSON, GZip
-
-BASEDIR = dirname(@__FILE__)
-
-@testset "Reports" begin
-    @testset "from solve" begin
-        solution = RELOG.solve(joinpath(BASEDIR, "..", "instances", "s1.json"))
-        tmp_filename = tempname()
-        # The following should not crash
-        RELOG.write_plant_emissions_report(solution, tmp_filename)
-        RELOG.write_plant_outputs_report(solution, tmp_filename)
-        RELOG.write_plants_report(solution, tmp_filename)
-        RELOG.write_products_report(solution, tmp_filename)
-        RELOG.write_transportation_emissions_report(solution, tmp_filename)
-        RELOG.write_transportation_report(solution, tmp_filename)
-    end
-end
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -1,21 +0,0 @@
-# Copyright (C) 2020 Argonne National Laboratory
-# Written by Alinson Santos Xavier <axavier@anl.gov>
-
-using Test
-
-@testset "RELOG" begin
-    @testset "Instance" begin
-        include("instance/compress_test.jl")
-        include("instance/geodb_test.jl")
-        include("instance/parse_test.jl")
-    end
-    @testset "Graph" begin
-        include("graph/build_test.jl")
-    end
-    @testset "Model" begin
-        include("model/build_test.jl")
-        include("model/solve_test.jl")
-        include("model/resolve_test.jl")
-    end
-    include("reports_test.jl")
-end
--- a/test/src/RELOGT.jl
+++ b/test/src/RELOGT.jl
@@ -0,0 +1,51 @@
+module RELOGT
+
+using Test
+using JuliaFormatter
+
+include("instance/compress_test.jl")
+include("instance/geodb_test.jl")
+include("instance/parse_test.jl")
+include("graph/build_test.jl")
+include("graph/dist_test.jl")
+include("model/build_test.jl")
+include("model/solve_test.jl")
+include("model/resolve_test.jl")
+include("reports_test.jl")
+
+basedir = dirname(@__FILE__)
+
+function fixture(path::String)::String
+    return "$basedir/../fixtures/$path"
+end
+
+function runtests()
+    @testset "RELOG" begin
+        @testset "instance" begin
+            instance_compress_test()
+            instance_geodb_test()
+            instance_parse_test()
+        end
+        @testset "graph" begin
+            graph_build_test()
+            graph_dist_test()
+        end
+        @testset "model" begin
+            model_build_test()
+            model_solve_test()
+            model_resolve_test()
+        end
+        reports_test()
+    end
+    return
+end
+
+function format()
+    JuliaFormatter.format(basedir, verbose = true)
+    JuliaFormatter.format("$basedir/../../src", verbose = true)
+    return
+end
+
+export runtests, format
+
+end # module RELOGT
--- a/test/src/graph/build_test.jl
+++ b/test/src/graph/build_test.jl
@@ -0,0 +1,40 @@
+# Copyright (C) 2020 Argonne National Laboratory
+# Written by Alinson Santos Xavier <axavier@anl.gov>
+
+using RELOG
+
+function graph_build_test()
+    @testset "build_graph" begin
+        instance = RELOG.parsefile(fixture("s1.json"))
+        graph = RELOG.build_graph(instance)
+        process_node_by_location_name =
+            Dict(n.location.location_name => n for n in graph.process_nodes)
+
+        @test length(graph.plant_shipping_nodes) == 8
+        @test length(graph.collection_shipping_nodes) == 10
+        @test length(graph.process_nodes) == 6
+
+        node = graph.collection_shipping_nodes[1]
+        @test node.location.name == "C1"
+        @test length(node.incoming_arcs) == 0
+        @test length(node.outgoing_arcs) == 2
+        @test node.outgoing_arcs[1].source.location.name == "C1"
+        @test node.outgoing_arcs[1].dest.location.plant_name == "F1"
+        @test node.outgoing_arcs[1].dest.location.location_name == "L1"
+        @test node.outgoing_arcs[1].values["distance"] == 1695.364
+
+        node = process_node_by_location_name["L1"]
+        @test node.location.plant_name == "F1"
+        @test node.location.location_name == "L1"
+        @test length(node.incoming_arcs) == 10
+        @test length(node.outgoing_arcs) == 2
+
+        node = process_node_by_location_name["L3"]
+        @test node.location.plant_name == "F2"
+        @test node.location.location_name == "L3"
+        @test length(node.incoming_arcs) == 2
+        @test length(node.outgoing_arcs) == 2
+
+        @test length(graph.arcs) == 38
+    end
+end
--- a/test/src/graph/dist_test.jl
+++ b/test/src/graph/dist_test.jl
@@ -0,0 +1,27 @@
+# RELOG: Reverse Logistics Optimization
+# Copyright (C) 2020, UChicago Argonne, LLC. All rights reserved.
+# Released under the modified BSD license. See COPYING.md for more details.
+
+using RELOG
+
+function graph_dist_test()
+    @testset "KnnDrivingDistance" begin
+        # Euclidean distance between Chicago and Indianapolis
+        @test RELOG._calculate_distance(
+            41.866,
+            -87.656,
+            39.764,
+            -86.148,
+            RELOG.EuclideanDistance(),
+        ) == 265.818
+
+        # Approximate driving distance between Chicago and Indianapolis
+        @test RELOG._calculate_distance(
+            41.866,
+            -87.656,
+            39.764,
+            -86.148,
+            RELOG.KnnDrivingDistance(),
+        ) == 316.43
+    end
+end
--- a/test/src/instance/compress_test.jl
+++ b/test/src/instance/compress_test.jl
@@ -0,0 +1,54 @@
+# Copyright (C) 2020 Argonne National Laboratory
+# Written by Alinson Santos Xavier <axavier@anl.gov>
+
+using RELOG
+
+function instance_compress_test()
+    @testset "compress" begin
+        instance = RELOG.parsefile(fixture("s1.json"))
+        compressed = RELOG._compress(instance)
+
+        product_name_to_product = Dict(p.name => p for p in compressed.products)
+        location_name_to_facility = Dict()
+        for p in compressed.plants
+            location_name_to_facility[p.location_name] = p
+        end
+        for c in compressed.collection_centers
+            location_name_to_facility[c.name] = c
+        end
+
+        p1 = product_name_to_product["P1"]
+        p2 = product_name_to_product["P2"]
+        p3 = product_name_to_product["P3"]
+        c1 = location_name_to_facility["C1"]
+        l1 = location_name_to_facility["L1"]
+
+        @test compressed.time == 1
+        @test compressed.building_period == [1]
+
+        @test p1.name == "P1"
+        @test p1.transportation_cost ≈ [0.015]
+        @test p1.transportation_energy ≈ [0.115]
+        @test p1.transportation_emissions["CO2"] ≈ [0.051]
+        @test p1.transportation_emissions["CH4"] ≈ [0.0025]
+
+        @test c1.name == "C1"
+        @test c1.amount ≈ [1869.12]
+
+        @test l1.plant_name == "F1"
+        @test l1.location_name == "L1"
+        @test l1.energy ≈ [0.115]
+        @test l1.emissions["CO2"] ≈ [0.051]
+        @test l1.emissions["CH4"] ≈ [0.0025]
+        @test l1.sizes[1].opening_cost ≈ [500]
+        @test l1.sizes[2].opening_cost ≈ [1250]
+        @test l1.sizes[1].fixed_operating_cost ≈ [60]
+        @test l1.sizes[2].fixed_operating_cost ≈ [60]
+        @test l1.sizes[1].variable_operating_cost ≈ [30]
+        @test l1.sizes[2].variable_operating_cost ≈ [30]
+        @test l1.disposal_limit[p2] ≈ [2.0]
+        @test l1.disposal_limit[p3] ≈ [2.0]
+        @test l1.disposal_cost[p2] ≈ [-10.0]
+        @test l1.disposal_cost[p3] ≈ [-10.0]
+    end
+end
--- a/test/src/instance/geodb_test.jl
+++ b/test/src/instance/geodb_test.jl
@@ -0,0 +1,27 @@
+# RELOG: Reverse Logistics Optimization
+# Copyright (C) 2020, UChicago Argonne, LLC. All rights reserved.
+# Released under the modified BSD license. See COPYING.md for more details.
+
+using RELOG
+
+function instance_geodb_test()
+    @testset "geodb_query (2018-us-county)" begin
+        region = RELOG.geodb_query("2018-us-county:17043")
+        @test region.centroid.lat == 41.83956
+        @test region.centroid.lon == -88.08857
+        @test region.population == 922_921
+    end
+
+    # @testset "geodb_query (2018-us-zcta)" begin
+    #     region = RELOG.geodb_query("2018-us-zcta:60439")
+    #     @test region.centroid.lat == 41.68241
+    #     @test region.centroid.lon == -87.98954
+    # end
+
+    @testset "geodb_query (us-state)" begin
+        region = RELOG.geodb_query("us-state:IL")
+        @test region.centroid.lat == 39.73939
+        @test region.centroid.lon == -89.50414
+        @test region.population == 12_671_821
+    end
+end
--- a/test/src/instance/parse_test.jl
+++ b/test/src/instance/parse_test.jl
@@ -0,0 +1,87 @@
+# Copyright (C) 2020 Argonne National Laboratory
+# Written by Alinson Santos Xavier <axavier@anl.gov>
+
+using RELOG
+
+function instance_parse_test()
+    @testset "parse" begin
+        instance = RELOG.parsefile(fixture("s1.json"))
+
+        centers = instance.collection_centers
+        plants = instance.plants
+        products = instance.products
+        location_name_to_plant = Dict(p.location_name => p for p in plants)
+        product_name_to_product = Dict(p.name => p for p in products)
+
+        @test length(centers) == 10
+        @test centers[1].name == "C1"
+        @test centers[1].latitude == 7
+        @test centers[1].latitude == 7
+        @test centers[1].longitude == 7
+        @test centers[1].amount == [934.56, 934.56]
+        @test centers[1].product.name == "P1"
+
+        @test length(plants) == 6
+
+        plant = location_name_to_plant["L1"]
+        @test plant.plant_name == "F1"
+        @test plant.location_name == "L1"
+        @test plant.input.name == "P1"
+        @test plant.latitude == 0
+        @test plant.longitude == 0
+
+        @test length(plant.sizes) == 2
+        @test plant.sizes[1].capacity == 250
+        @test plant.sizes[1].opening_cost == [500, 500]
+        @test plant.sizes[1].fixed_operating_cost == [30, 30]
+        @test plant.sizes[1].variable_operating_cost == [30, 30]
+        @test plant.sizes[2].capacity == 1000
+        @test plant.sizes[2].opening_cost == [1250, 1250]
+        @test plant.sizes[2].fixed_operating_cost == [30, 30]
+        @test plant.sizes[2].variable_operating_cost == [30, 30]
+
+        p1 = product_name_to_product["P1"]
+        @test p1.disposal_limit == [1.0, 1.0]
+        @test p1.disposal_cost == [-1000.0, -1000.0]
+
+        p2 = product_name_to_product["P2"]
+        @test p2.disposal_limit == [0.0, 0.0]
+        @test p2.disposal_cost == [0.0, 0.0]
+
+        p3 = product_name_to_product["P3"]
+        @test length(plant.output) == 2
+        @test plant.output[p2] == 0.2
+        @test plant.output[p3] == 0.5
+        @test plant.disposal_limit[p2] == [1, 1]
+        @test plant.disposal_limit[p3] == [1, 1]
+        @test plant.disposal_cost[p2] == [-10, -10]
+        @test plant.disposal_cost[p3] == [-10, -10]
+
+        plant = location_name_to_plant["L3"]
+        @test plant.location_name == "L3"
+        @test plant.input.name == "P2"
+        @test plant.latitude == 25
+        @test plant.longitude == 65
+
+        @test length(plant.sizes) == 2
+        @test plant.sizes[1].capacity == 1000.0
+        @test plant.sizes[1].opening_cost == [3000, 3000]
+        @test plant.sizes[1].fixed_operating_cost == [50, 50]
+        @test plant.sizes[1].variable_operating_cost == [50, 50]
+        @test plant.sizes[1] == plant.sizes[2]
+
+        p4 = product_name_to_product["P4"]
+        @test plant.output[p3] == 0.05
+        @test plant.output[p4] == 0.8
+        @test plant.disposal_limit[p3] == [1e8, 1e8]
+        @test plant.disposal_limit[p4] == [0, 0]
+    end
+
+    @testset "parse (geodb)" begin
+        instance = RELOG.parsefile(fixture("s2.json"))
+        centers = instance.collection_centers
+        @test centers[1].name == "C1"
+        @test centers[1].latitude == 41.83956
+        @test centers[1].longitude == -88.08857
+    end
+end
--- a/test/src/model/build_test.jl
+++ b/test/src/model/build_test.jl
@@ -0,0 +1,40 @@
+# Copyright (C) 2020 Argonne National Laboratory
+# Written by Alinson Santos Xavier <axavier@anl.gov>
+
+using RELOG, Cbc, JuMP, Printf, JSON, MathOptInterface.FileFormats
+
+function model_build_test()
+    @testset "build" begin
+        instance = RELOG.parsefile(fixture("s1.json"))
+        graph = RELOG.build_graph(instance)
+        model = RELOG.build_model(instance, graph, Cbc.Optimizer)
+        set_optimizer_attribute(model, "logLevel", 0)
+
+        process_node_by_location_name =
+            Dict(n.location.location_name => n for n in graph.process_nodes)
+
+        shipping_node_by_loc_and_prod_names = Dict(
+            (n.location.location_name, n.product.name) => n for
+            n in graph.plant_shipping_nodes
+        )
+
+        @test length(model[:flow]) == 76
+        @test length(model[:plant_dispose]) == 16
+        @test length(model[:open_plant]) == 12
+        @test length(model[:capacity]) == 12
+        @test length(model[:expansion]) == 12
+
+        l1 = process_node_by_location_name["L1"]
+        v = model[:capacity][l1, 1]
+        @test lower_bound(v) == 0.0
+        @test upper_bound(v) == 1000.0
+
+        v = model[:expansion][l1, 1]
+        @test lower_bound(v) == 0.0
+        @test upper_bound(v) == 750.0
+
+        v = model[:plant_dispose][shipping_node_by_loc_and_prod_names["L1", "P2"], 1]
+        @test lower_bound(v) == 0.0
+        @test upper_bound(v) == 1.0
+    end
+end
--- a/test/src/model/resolve_test.jl
+++ b/test/src/model/resolve_test.jl
@@ -0,0 +1,13 @@
+# Copyright (C) 2020 Argonne National Laboratory
+# Written by Alinson Santos Xavier <axavier@anl.gov>
+
+using RELOG
+
+function model_resolve_test()
+    @testset "Resolve" begin
+        # Shoud not crash
+        filename = fixture("s1.json")
+        solution_old, model_old = RELOG.solve(filename, return_model = true)
+        solution_new = RELOG.resolve(model_old, filename)
+    end
+end
--- a/test/src/model/solve_test.jl
+++ b/test/src/model/solve_test.jl
@@ -0,0 +1,70 @@
+# Copyright (C) 2020 Argonne National Laboratory
+# Written by Alinson Santos Xavier <axavier@anl.gov>
+
+using RELOG, Cbc, JuMP, Printf, JSON, MathOptInterface.FileFormats
+
+
+function model_solve_test()
+    @testset "solve (exact)" begin
+        solution_filename_a = tempname()
+        solution_filename_b = tempname()
+        solution = RELOG.solve(fixture("s1.json"), output = solution_filename_a)
+
+        @test isfile(solution_filename_a)
+
+        RELOG.write(solution, solution_filename_b)
+        @test isfile(solution_filename_b)
+
+        @test "Costs" in keys(solution)
+        @test "Fixed operating (\$)" in keys(solution["Costs"])
+        @test "Transportation (\$)" in keys(solution["Costs"])
+        @test "Variable operating (\$)" in keys(solution["Costs"])
+        @test "Total (\$)" in keys(solution["Costs"])
+
+        @test "Plants" in keys(solution)
+        @test "F1" in keys(solution["Plants"])
+        @test "F2" in keys(solution["Plants"])
+        @test "F3" in keys(solution["Plants"])
+        @test "F4" in keys(solution["Plants"])
+
+        @test "Products" in keys(solution)
+        @test "P1" in keys(solution["Products"])
+        @test "C1" in keys(solution["Products"]["P1"])
+        @test "Dispose (tonne)" in keys(solution["Products"]["P1"]["C1"])
+
+        total_disposal =
+            sum([loc["Dispose (tonne)"] for loc in values(solution["Products"]["P1"])])
+        @test total_disposal == [1.0, 1.0]
+    end
+
+    @testset "solve (heuristic)" begin
+        # Should not crash
+        solution = RELOG.solve(fixture("s1.json"), heuristic = true)
+    end
+
+    @testset "solve (infeasible)" begin
+        json = JSON.parsefile(fixture("s1.json"))
+        for (location_name, location_dict) in json["products"]["P1"]["initial amounts"]
+            location_dict["amount (tonne)"] *= 1000
+        end
+        @test_throws ErrorException("No solution available") RELOG.solve(RELOG.parse(json))
+    end
+
+    @testset "solve (with storage)" begin
+        filename = fixture("storage.json")
+        instance = RELOG.parsefile(filename)
+        @test instance.plants[1].storage_limit == 50.0
+        @test instance.plants[1].storage_cost == [2.0, 1.5, 1.0]
+
+        solution = RELOG.solve(filename)
+        plant_dict = solution["Plants"]["mega plant"]["Chicago"]
+        @test plant_dict["Variable operating cost (\$)"] == [500.0, 0.0, 100.0]
+        @test plant_dict["Process (tonne)"] == [50.0, 0.0, 50.0]
+        @test plant_dict["Storage (tonne)"] == [50.0, 50.0, 0.0]
+        @test plant_dict["Storage cost (\$)"] == [100.0, 75.0, 0.0]
+
+        @test solution["Costs"]["Variable operating (\$)"] == [500.0, 0.0, 100.0]
+        @test solution["Costs"]["Storage (\$)"] == [100.0, 75.0, 0.0]
+        @test solution["Costs"]["Total (\$)"] == [600.0, 75.0, 100.0]
+    end
+end
--- a/test/src/reports_test.jl
+++ b/test/src/reports_test.jl
@@ -0,0 +1,21 @@
+# RELOG: Reverse Logistics Optimization
+# Copyright (C) 2020, UChicago Argonne, LLC. All rights reserved.
+# Released under the modified BSD license. See COPYING.md for more details.
+
+using RELOG, JSON, GZip
+
+function reports_test()
+    @testset "reports" begin
+        @testset "from solve" begin
+            solution = RELOG.solve(fixture("s1.json"))
+            tmp_filename = tempname()
+            # The following should not crash
+            RELOG.write_plant_emissions_report(solution, tmp_filename)
+            RELOG.write_plant_outputs_report(solution, tmp_filename)
+            RELOG.write_plants_report(solution, tmp_filename)
+            RELOG.write_products_report(solution, tmp_filename)
+            RELOG.write_transportation_emissions_report(solution, tmp_filename)
+            RELOG.write_transportation_report(solution, tmp_filename)
+        end
+    end
+end
Author	SHA1	Message	Date
Alinson S. Xavier	7bce105428	Fix formatting	2023-02-15 13:47:00 -06:00
Alinson S. Xavier	1aa01b7b2b	Merge branch 'master' into relog-web	2023-02-15 13:27:47 -06:00
Alinson S. Xavier	e86ae0f818	Add RELOG.version()	2023-02-15 13:22:47 -06:00
Alinson S. Xavier	22d73c9ded	Move tests to a separate package; update GitHub CI and docs	2023-02-15 12:32:29 -06:00
Alinson S. Xavier	a8e4491ea3	Merge branch 'master' into feature/collection-disposal	2023-02-15 11:01:10 -06:00
Alinson S. Xavier	50d53f628f	Reformat source code	2023-01-24 10:31:40 -06:00
Alinson S. Xavier	79748e3c13	Dist: Drop NaN in training dataset	2023-01-24 10:27:41 -06:00
Alinson S. Xavier	d1f6796c96	Update CHANGELOG.md	2022-12-16 15:33:16 -06:00
Alinson S. Xavier	51ff8eb130	Restrict NearestNeighbors version; remove debug statement	2022-12-15 11:03:44 -06:00
Alinson S. Xavier	9191474df8	Bump version to 0.6	2022-12-15 10:36:44 -06:00
Alinson S. Xavier	841fbf16fb	Make distance metric configurable; fix building period bug	2022-12-15 10:26:10 -06:00
Alinson S. Xavier	48bd3c403f	Switch from Euclidean to approximate driving distance	2022-12-15 09:49:38 -06:00
Alinson S. Xavier	23b3b33146	Update README.md	2022-10-28 14:05:53 -05:00
Alinson S. Xavier	86dee7558b	Replace Cbc/Clp by HiGHS	2022-09-08 12:14:49 -05:00
Alinson S. Xavier	d84b74a8a7	relog-web: Make time limit configurable	2022-09-08 11:35:11 -05:00
Alinson S. Xavier	bae39a4ff4	Merge tag 'v0.5.2' into feature/gui [Diff since v0.5.1](https://github.com/ANL-CEEESA/RELOG/compare/v0.5.1...v0.5.2)	2022-08-26 14:34:17 -05:00
Alinson S. Xavier	da158eb961	Update CHANGELOG	2022-08-26 13:26:15 -05:00
Alinson S. Xavier	e7eec937cb	Update README.md	2022-08-26 13:21:42 -05:00
Alinson S. Xavier	19bec961bd	GH Actions: Update Julia versions	2022-08-26 13:12:20 -05:00
Alinson S. Xavier	8f52c04702	Fix broken image link	2022-08-26 13:08:22 -05:00
Alinson S. Xavier	19a34fb5d2	Update dependencies; switch to Documenter.jl	2022-08-26 13:04:47 -05:00
Alinson S Xavier	a03b9169fd	Allow product disposal at collection centers	2021-10-15 09:11:41 -05:00
Alinson S Xavier	ee58af73f0	Update sysimage and build scripts	2021-10-15 08:14:04 -05:00