Merge pull request #2 from pypsa-meets-earth/main

Merge from Upstream

.github/dependabot.yml

@@ -0,0 +1,14 @@
+# dependabot
+# Ref: https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+# ------------------------------------------------------------------------------
+version: 2
+updates:
+- package-ecosystem: github-actions
+  directory: /
+  schedule:
+    interval: daily
+  groups:
+    # open a single pull-request for all GitHub actions updates
+    github-actions:
+      patterns:
+      - '*'

.github/workflows/codeql.yml

@@ -0,0 +1,92 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["main"]
+  schedule:
+  - cron: '23 18 * * 5'
+
+jobs:
+  analyze:
+    name: Analyze (${{ matrix.language }})
+    # Runner size impacts CodeQL analysis time. To learn more, please see:
+    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
+    #   - https://gh.io/supported-runners-and-hardware-resources
+    #   - https://gh.io/using-larger-runners (GitHub.com only)
+    # Consider using larger runners or machines with greater resources for possible analysis time improvements.
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    permissions:
+      # required for all workflows
+      security-events: write
+
+      # required to fetch internal or private CodeQL packs
+      packages: read
+
+      # only required for workflows in private repositories
+      actions: read
+      contents: read
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - language: python
+          build-mode: none
+        # CodeQL supports the following values keywords for 'language': 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift'
+        # Use `c-cpp` to analyze code written in C, C++ or both
+        # Use 'java-kotlin' to analyze code written in Java, Kotlin or both
+        # Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
+        # To learn more about changing the languages that are analyzed or customizing the build mode for your analysis,
+        # see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning.
+        # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
+        # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: ${{ matrix.language }}
+        build-mode: ${{ matrix.build-mode }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+    # If the analyze step fails for one of the languages you are analyzing with
+    # "We were unable to automatically build your code", modify the matrix above
+    # to set the build mode to "manual" for that language. Then modify this step
+    # to build your code.
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+    - if: matrix.build-mode == 'manual'
+      shell: bash
+      run: |
+        echo 'If you are using a "manual" build mode for one or more of the' \
+          'languages you are analyzing, replace this with the commands to build' \
+          'your code, for example:'
+        echo '  make bootstrap'
+        echo '  make release'
+        exit 1
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:${{matrix.language}}"

.github/workflows/main.yml

@@ -1,14 +1,13 @@
 on:
-  push:
-    branches:
-    - main
+  schedule:
+  - cron: "0 5 * * 0"
 
 jobs:
   contrib-readme-job:
     runs-on: ubuntu-latest
     name: A job to automate contrib in readme
     steps:
     - name: Contribute List
-      uses: akhilmhdh/[email protected].6
+      uses: akhilmhdh/[email protected].10
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/ci.yml → .github/workflows/test.yml

@@ -1,4 +1,4 @@
-name: CI
+name: Test workflows
 
 on:
   push:
@@ -10,35 +10,43 @@ on:
   schedule:
   - cron: "0 5 * * TUE"
 
+# Cancel any in-progress runs when a new run is triggered
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 env:
-  CACHE_NUMBER: 2  # Change this value to manually reset the environment cache
+  CACHE_NUMBER: 0  # Change this value to manually reset the environment cache
 
 jobs:
-  build:
+  run-tests:
+    name: OS
+    runs-on: ${{ matrix.os }}-latest
     strategy:
       fail-fast: false
-      max-parallel: 3
       matrix:
-        os:
-        - ubuntu-latest
-        - macos-latest
-        # - windows-latest
-
-    runs-on: ${{ matrix.os }}
+        os: [ubuntu, macos] #, windows]
+        include:
+        - os: ubuntu
+          env_file: envs/linux-pinned.yaml
+        - os: macos
+          env_file: envs/macos-pinned.yaml
+        # - os: windows
+        #   env_file: envs/windows-pinned.yaml
 
     defaults:
       run:
         shell: bash -l {0}
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
 
     - name: Setup micromamba
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
         micromamba-version: '1.5.9-1'
-        environment-file: envs/environment.yaml
+        environment-file: ${{ matrix.env_file }}
         log-level: debug
         init-shell: bash
         cache-environment: true
@@ -50,7 +58,7 @@ jobs:
         echo "WEEK=$(date +'%Y%U')" >> $GITHUB_ENV
 
     - name: Cache data and cutouts folders
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
           data
@@ -64,6 +72,17 @@ jobs:
     - name: Run Test
       run: make test
 
+    - name: Upload artifacts
+      if: always()
+      uses: actions/upload-artifact@v4
+      with:
+        name: results-${{ matrix.os }}
+        path: |
+          logs
+          .snakemake/log
+          results
+        retention-days: 3
+
       # - name: Test plotting and summaries
       #   run: |
       #     snakemake --cores all plot_all_p_nom

.github/workflows/update-pinned-env.yml

@@ -0,0 +1,85 @@
+name: Update pinned envs
+
+on:
+  push:
+    paths:
+    - envs/environment.yaml
+  # Run every Sunday at 5:00 UTC
+  schedule:
+  - cron: "0 5 * * 0"
+  workflow_dispatch:
+
+
+jobs:
+  update-pinned-environment:
+    if: ${{ github.ref == 'refs/heads/main' }}
+    name: Update pinned envs
+    runs-on: ${{ matrix.os }}-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu, macos, windows]
+        include:
+        - os: ubuntu
+          suffix: "linux"
+        - os: macos
+          suffix: "macos"
+        - os: windows
+          suffix: "windows"
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Setup conda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        activate-environment: ${{ github.event.repository.name }}
+        environment-file: envs/environment.yaml
+
+    - name: Update pinned environment per OS
+      run: |
+        conda env export --name ${{ github.event.repository.name }} --no-builds > envs/${{ matrix.suffix }}-pinned.yaml
+
+    - name: Add SPDX header
+      if: ${{ matrix.suffix != 'windows' }}
+      run: |
+        SPDX_HEADER="# SPDX-FileCopyrightText: PyPSA-Earth and PyPSA-Eur Authors\n#\n# SPDX-License-Identifier: CC0-1.0\n"
+        echo -e "$SPDX_HEADER" | cat - envs/${{ matrix.suffix }}-pinned.yaml > temp && mv temp envs/${{ matrix.suffix }}-pinned.yaml
+
+    - name: Add SPDX header (windows)
+      if: ${{ matrix.suffix == 'windows' }}
+      run: |
+        $SPDX_HEADER = "# SPDX-FileCopyrightText: PyPSA-Earth and PyPSA-Eur`r`n#`r`n# SPDX-License-Identifier: CC0-1.0`r`n`r`n"
+        $CurrentContent = Get-Content "envs/${{ matrix.suffix }}-pinned.yaml" -Raw
+        $NewContent = $SPDX_HEADER + $CurrentContent
+        $NewContent | Set-Content "envs/${{ matrix.suffix }}-pinned.yaml"
+
+    - name: Cache environment files
+      uses: actions/upload-artifact@v4
+      with:
+        name: ${{ matrix.suffix }}-pinned
+        path: envs/${{ matrix.suffix }}-pinned.yaml
+
+  create-pull-request:
+    needs: update-pinned-environment
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Download all artifacts
+      uses: actions/download-artifact@v4
+
+    - name: Prepare files for commit
+      run: |
+        mkdir -p envs
+        mv linux-pinned/* envs/linux-pinned.yaml
+        mv macos-pinned/* envs/macos-pinned.yaml
+        mv windows-pinned/* envs/windows-pinned.yaml
+
+    - name: Create Pull Request
+      uses: peter-evans/create-pull-request@v7
+      with:
+        token: ${{ secrets.GITHUB_TOKEN }}
+        branch: update-pinned-environment
+        title: "[github-actions.ci] Update pinned envs"
+        body: "Automatically generated PR to update pinned environment files for Windows, macOS, and Linux."
+        commit-message: "Update pinned environment files for all platforms"

.pre-commit-config.yaml

@@ -35,12 +35,15 @@ repos:
     types_or: [python, rst, markdown]
     files: ^(scripts|doc)/
 
-# Make docstrings PEP 257 compliant
-- repo: https://github.com/PyCQA/docformatter
-  rev: v1.7.5
-  hooks:
-  - id: docformatter
-    args: ["--in-place", "--make-summary-multi-line", "--pre-summary-newline"]
+# # Make docstrings PEP 257 compliant
+# - repo: https://github.com/PyCQA/docformatter
+#   rev: v1.7.5
+#   hooks:
+#   - id: docformatter
+#     args: ["--in-place", "--make-summary-multi-line", "--pre-summary-newline"]
+#     entry: docformatter
+#     language: python
+#     types: [python]
 
 - repo: https://github.com/keewis/blackdoc
   rev: v0.3.9
@@ -87,6 +90,6 @@ repos:
 
 # Check for FSFE REUSE compliance (licensing)
 - repo: https://github.com/fsfe/reuse-tool
-  rev: v4.0.3
+  rev: v5.0.2
   hooks:
   - id: reuse