Merge branch 'develop' into 'master'

Develop into master See merge request iek-3/shared-code/fine!326
FZJ-IEK3-VSA · Feb 13, 2024 · f4ec7bb · f4ec7bb
2 parents a8f4a11 + 4666bc5
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -0,0 +1,86 @@
+on:
+  push:
+    branches:
+      - master
+      - develop
+  pull_request:
+    branches:
+      - master
+      - develop
+  # Allows to trigger the workflow manually
+  workflow_dispatch:
+    branches:
+      - master
+      - develop
+  schedule:
+    # * is a special character in YAML so you have to quote this string
+    # Some Examples for cron syntax https://crontab.guru/examples.html
+    # Schedules job at any point after 12 pm
+    - cron:  '0 0 * * *'
+    # Weekly after sunday
+    # - cron: 0 0 * * 0
+
+jobs:
+  TestFineSingle:
+    name: Ex1 (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          repository: FZJ-IEK3-VSA/FINE
+          path: './fine'
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-version: latest
+          channels: conda-forge
+          activate-environment: test_env
+      - name: Run tests
+        shell: pwsh
+        run: |
+          ls
+          echo "LS Done"
+          mamba install fine pytest
+          echo "Installation done"
+          conda list
+          echo "libaries printed"
+          echo "start pytest"
+          pytest
+          echo "Pytest done"
+
+  TestFineDevLocal:
+    name: Ex1 (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          repository: FZJ-IEK3-VSA/FINE
+          path: './fine'
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-version: latest
+          channels: conda-forge
+          activate-environment: test_env
+      - name: Run tests
+        shell: pwsh
+        run: |
+          ls
+          echo "LS Done"
+          cd fine
+          mamba env create --name fine_env --yes --file requirements_dev.yml
+          conda run --name fine_env pip install . --no-deps
+          echo "Installation done"
+          conda list --name fine_env
+          echo "libaries printed"
+          echo "start pytest"
+          conda run --name fine_env pytest
+          echo "Pytest done"
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -30,18 +30,20 @@ variables:
     policy: pull
   before_script:
     - micromamba install -n base -y --file=requirements_dev.yml
+    - python -m pip install .
   rules:
     # Switch from branch pipeline to merge pipeline once a merge request has
     # been created on the branch.
     - if: $CI_COMMIT_BRANCH && $CI_OPEN_MERGE_REQUESTS && $CI_PIPELINE_SOURCE == "push"
       when: never
     - if: $CI_COMMIT_BRANCH && $CI_OPEN_MERGE_REQUESTS
       when: never
+  retry: 1
 
 
 .test_docker_template_noupdate:
   stage: test
-  image: jugit-registry.fz-juelich.de/iek-3/shared-code/fine/fine-dev:latest 
+  image: jugit-registry.fz-juelich.de/iek-3/shared-code/fine/fine-dev:latest
   before_script:
     - python -m pip install -e .
   rules:
@@ -68,7 +70,7 @@ variables:
 
 .test_docker_template:
   stage: test
-  image: jugit-registry.fz-juelich.de/iek-3/shared-code/fine/fine-dev:latest 
+  image: jugit-registry.fz-juelich.de/iek-3/shared-code/fine/fine-dev:latest
   variables:
     CONDA_PKGS_DIRS: "$CI_PROJECT_DIR/.cache/pkgs"
   cache:
@@ -83,6 +85,7 @@ variables:
     policy: pull
   before_script:
     - micromamba install -n base -y --file=requirements_dev.yml
+    - python -m pip install .
   rules:
     # Do not run for pushes to master or develop and for merge requests to master
     - if: $CI_COMMIT_BRANCH == "master"
@@ -114,7 +117,7 @@ variables:
 test-code:
   extends: .test_template
   script:
-    - python -m pytest --cov=fine test/
+    - python -m pytest -n auto --cov=fine test/
   rules:
     # Run only for pushes to master or develop and for merge requests to master.
     # Do not run for scheduled pushes to master (runs `test-code-push-cache` instead).
@@ -129,20 +132,20 @@ test-code-push-cache:
   cache:
     policy: push
   script:
-    - python -m pytest --cov=fine test/
+    - python -m pytest -n auto --cov=fine test/
   rules:
     # Run only for scheduled pushes to master.
     - if: '$CI_PIPELINE_SOURCE == "schedule" && $CI_COMMIT_BRANCH == "master"'
 
 test-code-docker:
   extends: .test_docker_template
   script:
-    - python -m pytest --cov=fine test/
+    - python -m pytest -n auto --cov=fine test/
 
 test-code-docker-noupdate:
   extends: .test_docker_template_noupdate
   script:
-    - python -m pytest --cov=fine test/
+    - python -m pytest -n auto --cov=fine test/
 
 test-notebooks:
   extends: .test_template

diff --git a/README.md b/README.md
@@ -10,18 +10,35 @@
 
 # ETHOS.FINE - Framework for Integrated Energy System Assessment
 
+
 The ETHOS.FINE python package provides a framework for modeling, optimizing and assessing energy systems. With the provided framework, systems with multiple regions, commodities and time steps can be modeled. Target of the optimization is the minimization of the total annual cost while considering technical and environmental constraints. Besides using the full temporal resolution, an interconnected typical period storage formulation can be applied, that reduces the complexity and computational time of the model.
 
+This readme provides information on the installation of the package. For further information have a look at the [documentation](https://vsa-fine.readthedocs.io/en/latest/).
+
 ETHOS.FINE is used for the modelling of a diverse group of optimization problems within the [Energy Transformation PatHway Optimization Suite (ETHOS) at IEK-3](https://www.fz-juelich.de/de/iek/iek-3/leistungen/model-services).  
 
 If you want to use ETHOS.FINE in a published work, please [**kindly cite following publication**](https://www.sciencedirect.com/science/article/pii/S036054421830879X) which gives a description of the first stages of the framework. The python package which provides the time series aggregation module and its corresponding literature can be found [here](https://github.com/FZJ-IEK3-VSA/tsam).
 
-## Features
-* representation of an energy system by multiple locations, commodities and time steps
-* complexity reducing storage formulation based on typical periods
+## Content
+<!-- TOC -->
+* [Requirements](#requirements)
+  * [Python package manager](#python-package-manager)
+  * [Mixed Integer Linear Programming (MILP) solver](#mixed-integer-linear-programming-milp-solver)
+* [Installation](#installation)
+  * [Installation via conda-forge](#installation-via-conda-forge)
+  * [Installation from a local folder](#installation-from-a-local-folder)
+  * [Installation for developers](#installation-for-developers)
+* [Installation of an optimization solver](#installation-of-an-optimization-solver)
+  * [Gurobi installation](#gurobi-installation)
+  * [GLPK installation](#glpk-installation)
+  * [CBC](#cbc)
+* [Examples](#examples)
+* [License](#license)
+* [About Us](#about-us-)
+* [Contributions and Users](#contributions-and-users)
+* [Acknowledgement](#acknowledgement)
+<!-- TOC -->
 
-## Documentation
-A "Read the Docs" documentation of ETHOS.FINE can be found [here](https://vsa-fine.readthedocs.io/en/latest/).
 
 ## Requirements
 
@@ -46,7 +63,7 @@ mamba create -n fine -c conda-forge fine
 ### Installation from a local folder
 Alternatively you can first clone the content of this repository and perform the installation from there: 
 
-1. Clone the content of this repository 
+1. (Shallow) clone the content of this repository 
 ```bash
 git clone --depth 1 https://github.com/FZJ-IEK3-VSA/FINE.git 
 ```
@@ -62,14 +79,25 @@ mamba env create -f requirements.yml
 ```bash
 mamba activate fine
 ```
+6. Install FINE with:
+```bash
+python -m pip install --no-deps .
+```
 
 ### Installation for developers
 If you want to work on the FINE codebase you need to run. 
 ```bash
+git clone https://github.com/FZJ-IEK3-VSA/FINE.git
+```
+to get the whole git history and then
+```bash
 mamba env create -f requirements_dev.yml
 ```
 This installs additional dependencies such as `pytest` and installs FINE from the folder in editable mode with `pip -e`. Changes in the folder are then reflected in the package installation.
-
+Finally, install FINE in editable mode with:
+```bash
+python -m pip install --no-deps --editable .
+```
 Test your installation with the following command in the project root folder:
 ```
 pytest

diff --git a/docs/source/newsDoc.rst b/docs/source/newsDoc.rst
@@ -2,6 +2,8 @@
 FINE's News Feed
 ################
 
+Since version 2.3.3 this news feed is not updated anymore. Please refer to the [release page](https://github.com/FZJ-IEK3-VSA/FINE/releases) for changelogs.
+
 *********************
 Release version 2.3.2
 *********************

diff --git a/fine/IOManagement/standardIO.py b/fine/IOManagement/standardIO.py
@@ -95,7 +95,7 @@ def writeOptimizationOutputToExcel(
             if not optSum.empty:
                 optSum.to_excel(
                     writer,
-                    name[:-5]
+                    sheet_name=name[:-5]
                     + "OptSummary_"
                     + esM.componentModelingDict[name].dimension,
                 )
@@ -123,7 +123,7 @@ def writeOptimizationOutputToExcel(
                         ((dfTD1dim != 0) & (~dfTD1dim.isnull())).any(axis=1)
                     ]
                 if not dfTD1dim.empty:
-                    dfTD1dim.to_excel(writer, name[:-5] + "_TDoptVar_1dim")
+                    dfTD1dim.to_excel(writer, sheet_name=name[:-5] + "_TDoptVar_1dim")
             if dataTD2dim:
                 names = ["Variable", "Component", "LocationIn", "LocationOut"]
                 dfTD2dim = pd.concat(dataTD2dim, keys=indexTD2dim, names=names)
@@ -132,7 +132,7 @@ def writeOptimizationOutputToExcel(
                         ((dfTD2dim != 0) & (~dfTD2dim.isnull())).any(axis=1)
                     ]
                 if not dfTD2dim.empty:
-                    dfTD2dim.to_excel(writer, name[:-5] + "_TDoptVar_2dim")
+                    dfTD2dim.to_excel(writer, sheet_name=name[:-5] + "_TDoptVar_2dim")
             if dataTI:
                 if esM.componentModelingDict[name].dimension == "1dim":
                     names = ["Variable type", "Component"]
@@ -144,7 +144,7 @@ def writeOptimizationOutputToExcel(
                 if not dfTI.empty:
                     dfTI.to_excel(
                         writer,
-                        name[:-5]
+                        sheet_name=name[:-5]
                         + "_TIoptVar_"
                         + esM.componentModelingDict[name].dimension,
                     )
@@ -154,7 +154,7 @@ def writeOptimizationOutputToExcel(
         periodsOrder = pd.DataFrame(
             [esM.periodsOrder[_ip]], index=["periodsOrder"], columns=esM.periods
         )
-        periodsOrder.to_excel(writer, "Misc")
+        periodsOrder.to_excel(writer, sheet_name="Misc")
         if esM.segmentation:
             ls = []
             for i in esM.periodsOrder[_ip].tolist():
@@ -163,7 +163,7 @@ def writeOptimizationOutputToExcel(
                 columns={"Segment Duration": "timeStepsPerSegment"}
             )
             segmentDuration.index.name = "segmentNumber"
-            segmentDuration.to_excel(writer, "Misc", startrow=3)
+            segmentDuration.to_excel(writer, sheet_name="Misc", startrow=3)
         utils.output("\tSaving file...", esM.verbose, 0)
         writer.close()
         utils.output("Done. (%.4f" % (time.time() - _t) + " sec)", esM.verbose, 0)
@@ -809,7 +809,7 @@ def plotLocations(
     locationsShapeFileName,
     indexColumn,
     plotLocNames=False,
-    crs="epsg:3035",
+    crs="EPSG:3035",
     faceColor="none",
     edgeColor="black",
     fig=None,
@@ -840,7 +840,7 @@ def plotLocations(
     :type plotLocNames: boolean
 
     :param crs: coordinate reference system
-        |br| * the default value is 'epsg:3035'
+        |br| * the default value is 'EPSG:3035'
     :type crs: string
 
     :param faceColor: face color of the plot
@@ -884,7 +884,7 @@ def plotLocations(
     :type dpi: scalar > 0
     """
 
-    gdf = gpd.read_file(locationsShapeFileName).to_crs({"init": crs})
+    gdf = gpd.read_file(locationsShapeFileName).to_crs(crs)
 
     if ax is None:
         fig, ax = plt.subplots(1, 1, figsize=figsize, **kwargs)
@@ -919,7 +919,7 @@ def plotTransmission(
     loc0,
     loc1,
     ip=0,
-    crs="epsg:3035",
+    crs="EPSG:3035",
     variableName="capacityVariablesOptimum",
     color="k",
     loc=7,
@@ -961,7 +961,7 @@ def plotTransmission(
     :type ip: int
 
     :param crs: coordinate reference system
-        |br| * the default value is 'epsg:3035'
+        |br| * the default value is 'EPSG:3035'
     :type crs: string
 
     :param variableName: parameter for plotting installed capacity ('_capacityVariablesOptimum') or operation
@@ -1024,7 +1024,7 @@ def plotTransmission(
     if capMax == 0:
         return fig, ax
     cap = cap / capMax
-    gdf = gpd.read_file(transmissionShapeFileName).to_crs({"init": crs})
+    gdf = gpd.read_file(transmissionShapeFileName).to_crs(crs)
 
     if ax is None:
         fig, ax = plt.subplots(1, 1, figsize=figsize, **kwargs)
@@ -1082,7 +1082,7 @@ def plotLocationalColorMap(
     ip=0,
     perArea=True,
     areaFactor=1e3,
-    crs="epsg:3035",
+    crs="EPSG:3035",
     variableName="capacityVariablesOptimum",
     doSum=False,
     cmap="viridis",
@@ -1128,7 +1128,7 @@ def plotLocationalColorMap(
     :type areaFactor: scalar > 0
 
     :param crs: coordinate reference system
-        |br| * the default value is 'epsg:3035'
+        |br| * the default value is 'EPSG:3035'
     :type crs: string
 
     :param variableName: parameter for plotting installed capacity ('_capacityVariablesOptimum') or operation
@@ -1184,7 +1184,7 @@ def plotLocationalColorMap(
 
     if doSum:
         data = data.sum(axis=1)
-    gdf = gpd.read_file(locationsShapeFileName).to_crs({"init": crs})
+    gdf = gpd.read_file(locationsShapeFileName).to_crs(crs)
 
     # Make sure the data and gdf indices match
     ## 1. Sort the indices to obtain same order