modelblocks-org · irm-codebase · Jun 24, 2026 · Jun 24, 2026 · Jun 24, 2026
diff --git a/.all-contributorsrc b/.all-contributorsrc
@@ -0,0 +1,16 @@
+{
+  "projectName": "module_co2stop_cdr",
+  "projectOwner": "modelblocks-org",
+  "repoType": "github",
+  "repoHost": "https://github.com",
+  "files": [
+    "README.md"
+  ],
+  "imageSize": 100,
+  "commit": false,
+  "commitConvention": "none",
+  "contributors": [],
+  "contributorsPerLine": 7,
+  "linkToUsage": false,
+  "contributorsSortAlphabetically": true
+}
diff --git a/.copier-answers.yml b/.copier-answers.yml
@@ -1,13 +1,13 @@
 # Changes here will be overwritten by Copier
 # !!!!! DO NOT MANUALLY MODIFY THIS FILE !!!!!
-_commit: latest
+_commit: v1.0.2
 _src_path: https://github.com/modelblocks-org/data-module-template.git
 author_email: i.ruizmanuel@tudelft.nl
 author_family_name: Ruiz Manuel
 author_given_name: Ivan
 github_org: modelblocks-org
 license: Apache-2.0
 module_description: A module to aggregate CDR potential in Europe into flexible spatial
-    resolutions, using the CO2Stop dataset
+    resolutions, using the CO2Stop dataset.
 module_long_name: Module CO2Stop - Carbon Dioxide Removal in Europe
 module_short_name: module_co2stop_cdr
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -8,13 +8,13 @@ assignees: ''
 ---
 
 **Describe the bug**
-A clear and concise description of what the bug is.
+A clear and concise description of the bug.
 
-**To Reproduce**
+**Steps to reproduce**
 Steps to reproduce the behavior:
 1. Go to '...'
-2. Click on '....'
-3. Scroll down to '....'
+2. Run '...'
+3. Provide '...'
 4. See error
 
 **Expected behavior**
@@ -23,9 +23,9 @@ A clear and concise description of what you expected to happen.
 **Screenshots**
 If applicable, add screenshots to help explain your problem.
 
-**Desktop (please complete the following information):**
+**Environment (please complete the following information):**
  - OS: [e.g. Linux Fedora 43, Windows 11...]
- - Version [e.g. v0.1.1]
+ - Version: [e.g. v0.1.1]
 
 **Additional context**
 Add any other context about the problem here.
diff --git a/.github/ISSUE_TEMPLATE/config.yaml b/.github/ISSUE_TEMPLATE/config.yaml
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
@@ -0,0 +1,11 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Modelblocks project website
+    url: https://www.modelblocks.org/
+    about: Consult our website for general information on our initiative.
+  - name: Documentation
+    url: https://modelblocks.readthedocs.io/
+    about: Read our documentation for general questions and guidelines.
+  - name: Community chat
+    url: https://calliope-modelblocks.zulipchat.com
+    about: Reach out to our community on our official Zulip chat.
diff --git a/.github/workflows/check-version.yml b/.github/workflows/check-version.yml
@@ -1,9 +1,75 @@
-# Check for changes in the upstream template. If changes are found, an issue is created
-name: Template check.
+# Check for changes in the upstream template. If changes are found, an issue is created.
+name: Template check
+
 on:
+  workflow_dispatch:
   schedule:
     - cron: '0 0 1 * *' # Runs at 00:00 UTC on the 1st day of every month
 
+defaults:
+  run:
+    shell: bash --noprofile --norc -euo pipefail {0}
+
 jobs:
-  copier-update:
-    uses: modelblocks-org/data-module-template/.github/workflows/template-check-version.yml@latest
+  copier-check-update:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      issues: write
+    env:
+      ISSUE_TITLE: Template update available
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Check for template updates
+        id: copier_check_update
+        run: |
+          update_json="$(uvx --from 'copier>=9.15.2' copier check-update --output-format json)"
+          echo "$update_json"
+          {
+            echo "update_available=$(jq -r '.update_available // false' <<< "$update_json")"
+            echo "current_version=$(jq -r '.current_version // "unknown"' <<< "$update_json")"
+            echo "latest_version=$(jq -r '.latest_version // "unknown"' <<< "$update_json")"
+          } >> "$GITHUB_OUTPUT"
+
+      - name: Check for existing update issue
+        if: steps.copier_check_update.outputs.update_available == 'true'
+        id: existing_issue
+        run: |
+          issue_count="$(gh issue list \
+            --repo "${{ github.repository }}" \
+            --state open \
+            --search "$ISSUE_TITLE in:title" \
+            --json title \
+            --jq "map(select(.title == \"$ISSUE_TITLE\")) | length")"
+          if [[ "$issue_count" -gt 0 ]]; then
+            echo "exists=true" >> "$GITHUB_OUTPUT"
+          else
+            echo "exists=false" >> "$GITHUB_OUTPUT"
+          fi
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Open update issue
+        if: steps.copier_check_update.outputs.update_available == 'true' && steps.existing_issue.outputs.exists != 'true'
+        run: |
+          gh issue create \
+            --repo "${{ github.repository }}" \
+            --title "$ISSUE_TITLE" \
+            --body "A new version of the Modelblocks data module template is available.
+
+          Current template version: ${{ steps.copier_check_update.outputs.current_version }}
+          Latest template version: ${{ steps.copier_check_update.outputs.latest_version }}
+
+          Please update this project using:
+
+          \`\`\`shell
+          copier update --skip-answered --defaults
+          \`\`\`
+
+          Review the resulting changes before merging them."
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/pr-ci.yml b/.github/workflows/pr-ci.yml
@@ -13,11 +13,10 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.12"]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
       - name: Setup pixi
-        uses: prefix-dev/setup-pixi@v0.8.3
+        uses: prefix-dev/setup-pixi@v0.9.6
       - name: Run integration tests
         id: tests
         run: pixi run test-integration
@@ -30,10 +29,10 @@ jobs:
         continue-on-error: true
       - name: Save integration logs
         if: ${{ always() }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: integration-test-logs-${{ matrix.os }}
-          path: tests/integration/results/integration_test/logs
+          path: tests/integration/resources/module/logs
           if-no-files-found: ignore
           retention-days: 30
       - name: Fail if integration or linting failed

diff --git a/.gitignore b/.gitignore
@@ -12,7 +12,8 @@ __pycache__
 *.pyc
 
 ### Environments
-.pixi/
+.pixi/*
+!.pixi/.gitignore
 
 ### Snakemake
 .snakemake/

diff --git a/.pixi/.gitignore b/.pixi/.gitignore
@@ -0,0 +1,3 @@
+*
+!.gitignore
+!config.toml
diff --git a/.pixi/config.toml b/.pixi/config.toml
@@ -0,0 +1 @@
+pinning-strategy = "latest-up"
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -25,15 +25,15 @@ repos:
 
   # Python file formatting
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.9
+    rev: v0.15.18
     hooks:
-      - id: ruff
+      - id: ruff-check
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
 
   # Snakemake file formatting
   - repo: https://github.com/snakemake/snakefmt
-    rev: v1.0.0
+    rev: v2.0.2
     hooks:
       - id: snakefmt
 
@@ -46,5 +46,5 @@ repos:
         args:  # these come from CO2Stop itself
           - --ignore-words-list=aproximated
 
-ci: # https://pre-commit.ci/
+ci:  # https://pre-commit.ci/
   autoupdate_schedule: quarterly
diff --git a/AUTHORS b/AUTHORS
@@ -2,6 +2,6 @@ This is the list of contributors for copyright purposes.
 
 This does not necessarily list everyone who has contributed to this software's
 code or documentation. For a full contributor list, see:
-<https://github.com/calliope-project/module_co2stop_cdr/graphs/contributors>
+<https://github.com/modelblocks-org/module_co2stop_cdr/graphs/contributors>
 
 Ivan Ruiz Manuel, <i.ruizmanuel@tudelft.nl>
diff --git a/CITATION.cff b/CITATION.cff
@@ -3,8 +3,8 @@
 # https://citation-file-format.github.io/
 cff-version: 1.2.0
 message: If you use this software or data produced by it, please cite it using the metadata from this file.
-title: "clio - module_co2stop_cdr: Module CO2Stop - Carbon Dioxide Removal"
-repository: "https://github.com/calliope-project/module_co2stop_cdr"
+title: "Modelblocks - module_co2stop_cdr: Module CO2Stop - Carbon Dioxide Removal in Europe"
+repository: "https://github.com/modelblocks-org/module_co2stop_cdr"
 license: Apache-2.0
 authors:
   - given-names: Ivan

diff --git a/INTERFACE.yaml b/INTERFACE.yaml
@@ -1,15 +1,17 @@
-# Module Input-Output structure for automated doc. generation
+# Module Input-Output structure for automated docs generation
+convention_version: v1.0.0
+
 pathvars:
   snakemake_defaults:
     logs:
       default: "<logs>"
-      description: location of rule log files.
+      description: location of snakemake log files.
     resources:
       default: "<resources>"
-      description: "location of module resource files."
+      description: "location of module resource (input) files."
     results:
       default: "<results>"
-      description: "location of module results."
+      description: "location of module result (output) files."
   user_resources:
     user_shapes:
       default: "<resources>/user/{shapes}/shapes.parquet"

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # Module CO2Stop - Carbon Dioxide Removal in Europe
 
-A module to aggregate CDR potential in Europe into flexible spatial resolutions, using the CO2Stop dataset
+A module to aggregate CDR potential in Europe into flexible spatial resolutions, using the CO2Stop dataset.
 
 <!-- Place an attractive image of module outputs here -->
 <p align="center">
@@ -81,6 +81,21 @@ cd module_co2stop_cdr
 pixi install --all
 ```
 
+Please be aware that this is a multi-environment project (see [pixi.toml](./pixi.toml) for details).
+- `default`: used for development and integration testing.
+Because it contains `Snakemake`, `conda` and `pytest` as dependencies it **should not be used** in `Snakemake` rules.
+- `module`: contains minimal dependencies used in `Snakemake` rules.
+If modified, be sure to export it to `Snakemake` so it can be recreated by module users:
+
+```shell
+# create module.yaml and conda-spec pin files in workflow/envs/
+pixi run export-snakemake-env module
+```
+
+
+## Testing
+<!-- Please do not modify this templated section -->
+
 For testing, simply run:
 
 ```shell
@@ -106,3 +121,16 @@ Poulsen, N., Holloway, S., Neele, F., Smith, N.A., Kirk, K., 2012. CO2StoP Execu
 Ruiz Manuel, I. clio - module_geo_boundaries [Computer software]. <https://github.com/calliope-project/module_geo_boundaries/>.
 - **Filtering minimum defaults:**
 Van Den Broek, M., Brederode, E., Ramírez, A., Kramers, L., Van Der Kuip, M., Wildenborg, T., Turkenburg, W., Faaij, A., 2010. Designing a cost-effective CO2 storage infrastructure using a GIS based linear optimization energy model. Environmental Modelling & Software 25, 1754–1768. <https://doi.org/10.1016/j.envsoft.2010.06.015>.
+
+## Contributors ✨
+
+Thanks goes to these wonderful people, sorted alphabetically ([emoji key](https://allcontributors.org/en/reference/emoji-key/)):
+
+<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
+<!-- prettier-ignore-start -->
+<!-- markdownlint-disable -->
+<!-- markdownlint-restore -->
+<!-- prettier-ignore-end -->
+<!-- ALL-CONTRIBUTORS-LIST:END -->
+
+This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!
diff --git a/figures/.gitkeep b/figures/.gitkeep
@@ -0,0 +1 @@
+# For module documentation figures