From 935929bc4f884b0814fdee64a7ac7d69b205cd85 Mon Sep 17 00:00:00 2001
From: Ivan Ruiz Manuel <72193617+irm-codebase@users.noreply.github.com>
Date: Wed, 24 Jun 2026 20:20:13 +0200
Subject: [PATCH 1/2] move to convention v1.0.0

---
 .all-contributorsrc                           |    16 +
 .copier-answers.yml                           |     4 +-
 .github/ISSUE_TEMPLATE/bug_report.md          |    12 +-
 .github/ISSUE_TEMPLATE/config.yaml            |     5 -
 .github/ISSUE_TEMPLATE/config.yml             |    11 +
 .github/workflows/check-version.yml           |    74 +-
 .github/workflows/pr-ci.yml                   |     9 +-
 .gitignore                                    |     3 +-
 .pixi/.gitignore                              |     3 +
 .pixi/config.toml                             |     1 +
 .pre-commit-config.yaml                       |     8 +-
 AUTHORS                                       |     2 +-
 CITATION.cff                                  |     4 +-
 INTERFACE.yaml                                |    10 +-
 README.md                                     |    30 +-
 figures/.gitkeep                              |     1 +
 pixi.lock                                     | 24564 +++++++++-------
 pixi.toml                                     |    67 +-
 tests/conftest.py                             |    23 +
 tests/integration/Snakefile                   |     6 +-
 tests/integration_test.py                     |    55 +-
 workflow/Snakefile                            |     2 +-
 workflow/envs/co2stop.yaml                    |    20 -
 ...nux-64.pin.txt => module.linux-64.pin.txt} |   185 +-
 ...arm64.pin.txt => module.osx-arm64.pin.txt} |   135 +-
 ...p.win-64.pin.txt => module.win-64.pin.txt} |   158 +-
 workflow/envs/module.yaml                     |    22 +
 workflow/envs/shell.yaml                      |     6 -
 workflow/rules/aggregate.smk                  |     4 +-
 workflow/rules/automatic.smk                  |     4 +-
 workflow/rules/prepare.smk                    |     4 +-
 31 files changed, 13868 insertions(+), 11580 deletions(-)
 create mode 100644 .all-contributorsrc
 delete mode 100644 .github/ISSUE_TEMPLATE/config.yaml
 create mode 100644 .github/ISSUE_TEMPLATE/config.yml
 create mode 100644 .pixi/.gitignore
 create mode 100644 .pixi/config.toml
 create mode 100644 figures/.gitkeep
 delete mode 100644 workflow/envs/co2stop.yaml
 rename workflow/envs/{co2stop.linux-64.pin.txt => module.linux-64.pin.txt} (73%)
 rename workflow/envs/{co2stop.osx-arm64.pin.txt => module.osx-arm64.pin.txt} (75%)
 rename workflow/envs/{co2stop.win-64.pin.txt => module.win-64.pin.txt} (69%)
 create mode 100644 workflow/envs/module.yaml
 delete mode 100644 workflow/envs/shell.yaml

diff --git a/.all-contributorsrc b/.all-contributorsrc
new file mode 100644
index 0000000..0a34405
--- /dev/null
+++ 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
index 637d40c..4dd536b 100644
--- a/.copier-answers.yml
+++ b/.copier-answers.yml
@@ -1,6 +1,6 @@
 # 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
@@ -8,6 +8,6 @@ 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
index 1b66ddc..6fe23c7 100644
--- 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
deleted file mode 100644
index 28da94d..0000000
--- a/.github/ISSUE_TEMPLATE/config.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-blank_issues_enabled: false
-contact_links:
-  - name: General information
-    url: https://www.modelblocks.org/
-    about: Please consult our website for general information on the Modelblocks methodology.
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
new file mode 100644
index 0000000..b68f870
--- /dev/null
+++ 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
index 0a4a602..04e53c3 100644
--- 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
index 728b9c5..18c5f00 100644
--- 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
index f03928b..7210c19 100644
--- 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
new file mode 100644
index 0000000..8399391
--- /dev/null
+++ b/.pixi/.gitignore
@@ -0,0 +1,3 @@
+*
+!.gitignore
+!config.toml
diff --git a/.pixi/config.toml b/.pixi/config.toml
new file mode 100644
index 0000000..a6a577c
--- /dev/null
+++ b/.pixi/config.toml
@@ -0,0 +1 @@
+pinning-strategy = "latest-up"
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 10954ae..510328f 100644
--- 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
index 24f9d0e..4d2b672 100644
--- 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
index 20534ac..1f16a28 100644
--- 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
index 6849955..3f0ba82 100644
--- 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
index 93bf706..a6334a5 100644
--- 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
new file mode 100644
index 0000000..dcafcbe
--- /dev/null
+++ b/figures/.gitkeep
@@ -0,0 +1 @@
+# For module documentation figures
diff --git a/pixi.lock b/pixi.lock
index 6135bfa..45d06e3 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -1,814 +1,348 @@
-version: 6
+version: 7
+platforms:
+- name: linux-64
+- name: osx-arm64
+- name: win-64
 environments:
-  co2stop:
+  default:
     channels:
     - url: https://conda.anaconda.org/conda-forge/
-    options:
-      pypi-prerelease-mode: if-necessary-or-explicit
+    - url: https://conda.anaconda.org/bioconda/
     packages:
       linux-64:
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.15.3-hb03c661_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/asttokens-3.0.1-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-auth-0.9.3-hef928c7_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.9.13-h2c9d079_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.12.6-hb03c661_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-compression-0.3.1-h8b1a151_9.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-event-stream-0.5.7-h28f887f_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-http-0.10.7-ha8fc4e3_5.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-io-0.23.3-hdaf4b65_5.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-mqtt-0.13.3-hc63082f_11.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-s3-0.11.3-h06ab39a_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-sdkutils-0.2.4-h8b1a151_4.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-checksums-0.2.7-h8b1a151_5.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-crt-cpp-0.35.4-h8824e59_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-sdk-cpp-1.11.606-h20b40b1_10.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-core-cpp-1.16.2-h206d751_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-identity-cpp-1.13.3-hed0cdb0_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-blobs-cpp-12.16.0-hdd73cc9_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-common-cpp-12.12.0-ha7a2c86_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-files-datalake-cpp-12.14.0-h52c5a47_1.conda
+      - conda: https://conda.anaconda.org/bioconda/noarch/snakefmt-0.11.3-pyha6daafd_0.conda
+      - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.22.0-pyhd4c3c12_0.conda
+      - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-executor-plugins-9.3.9-pyhdfd78af_0.tar.bz2
+      - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-logger-plugins-2.0.0-pyhd4c3c12_0.conda
+      - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-report-plugins-1.3.0-pyhd4c3c12_0.conda
+      - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-scheduler-plugins-2.0.2-pyhd4c3c12_0.conda
+      - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-storage-plugins-4.3.2-pyhd4c3c12_0.conda
+      - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-minimal-9.23.1-pyhdfd78af_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/at-spi2-atk-2.38.0-h0630a04_3.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/at-spi2-core-2.40.3-h0630a04_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/atk-1.0-2.38.0-h04ea711_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/backports.zstd-1.3.0-py313h18e8e13_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/blosc-1.21.6-he440d0b_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/branca-0.8.2-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-1.2.0-hed03a55_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.2.0-hb03c661_1.conda
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   license_family: BSD
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-  timestamp: 1769434732453
-- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-xorgproto-2025.1-hb03c661_0.conda
-  sha256: 7a8c64938428c2bfd016359f9cb3c44f94acc256c6167dbdade9f2a1f5ca7a36
-  md5: aa8d21be4b461ce612d8f5fb791decae
-  depends:
-  - __glibc >=2.17,<3.0.a0
-  - libgcc >=14
-  license: MIT
-  license_family: MIT
-  size: 570010
-  timestamp: 1766154256151
-- conda: https://conda.anaconda.org/conda-forge/noarch/xyzservices-2026.3.0-pyhd8ed1ab_0.conda
-  sha256: 663ea9b00d68c2da309114923924686ab6d3f59ef1b196c5029ba16799e7bb07
-  md5: 4487b9c371d0161d54b5c7bbd890c0fc
-  depends:
-  - python >=3.9
-  license: BSD-3-Clause
-  license_family: BSD
-  size: 51732
-  timestamp: 1774900074457
-- conda: https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h280c20c_3.conda
-  sha256: 6d9ea2f731e284e9316d95fa61869fe7bbba33df7929f82693c121022810f4ad
-  md5: a77f85f77be52ff59391544bfe73390a
-  depends:
-  - libgcc >=14
-  - __glibc >=2.17,<3.0.a0
-  license: MIT
-  license_family: MIT
-  size: 85189
-  timestamp: 1753484064210
-- conda: https://conda.anaconda.org/conda-forge/osx-arm64/yaml-0.2.5-h925e9cb_3.conda
-  sha256: b03433b13d89f5567e828ea9f1a7d5c5d697bf374c28a4168d71e9464f5dafac
-  md5: 78a0fe9e9c50d2c381e8ee47e3ea437d
-  depends:
-  - __osx >=11.0
-  license: MIT
-  license_family: MIT
-  size: 83386
-  timestamp: 1753484079473
 - conda: https://conda.anaconda.org/conda-forge/win-64/yaml-0.2.5-h6a83c73_3.conda
   sha256: 80ee68c1e7683a35295232ea79bcc87279d31ffeda04a1665efdb43cbd50a309
   md5: 433699cba6602098ae8957a323da2664
@@ -13641,28 +15897,6 @@ packages:
   license_family: MIT
   size: 63944
   timestamp: 1753484092156
-- conda: https://conda.anaconda.org/conda-forge/linux-64/yaml-cpp-0.8.0-h3f2d84a_0.conda
-  sha256: 4b0b713a4308864a59d5f0b66ac61b7960151c8022511cdc914c0c0458375eca
-  md5: 92b90f5f7a322e74468bb4909c7354b5
-  depends:
-  - libstdcxx >=13
-  - libgcc >=13
-  - __glibc >=2.17,<3.0.a0
-  - libgcc >=13
-  license: MIT
-  license_family: MIT
-  size: 223526
-  timestamp: 1745307989800
-- conda: https://conda.anaconda.org/conda-forge/osx-arm64/yaml-cpp-0.8.0-ha1acc90_0.conda
-  sha256: 66ba31cfb8014fdd3456f2b3b394df123bbd05d95b75328b7c4131639e299749
-  md5: 30475b3d0406587cf90386a283bb3cd0
-  depends:
-  - libcxx >=18
-  - __osx >=11.0
-  license: MIT
-  license_family: MIT
-  size: 136222
-  timestamp: 1745308075886
 - conda: https://conda.anaconda.org/conda-forge/win-64/yaml-cpp-0.8.0-he0c23c2_0.conda
   sha256: 031642d753e0ebd666a76cea399497cc7048ff363edf7d76a630ee0a19e341da
   md5: 9bb5064a9fca5ca8e7d7f1ae677354b6
@@ -13677,44 +15911,6 @@ packages:
   license_family: MIT
   size: 148572
   timestamp: 1745308037198
-- conda: https://conda.anaconda.org/conda-forge/noarch/yte-1.9.4-pyhd8ed1ab_0.conda
-  sha256: 1ad021f32290e72b70a84dfe0c9b278c61aaa1254f1e1c287d68c32ee4f1093f
-  md5: 89d5edf5d52d3bc1ed4d7d3feef508ba
-  depends:
-  - argparse-dataclass >=2.0.0,<3
-  - dpath >=2.1,<3.0
-  - python >=3.10
-  - pyyaml >=6.0,<7.0
-  license: MIT
-  license_family: MIT
-  size: 16215
-  timestamp: 1764250734338
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zeromq-4.3.5-h387f397_9.conda
-  sha256: 47cfe31255b91b4a6fa0e9dbaf26baa60ac97e033402dbc8b90ba5fee5ffe184
-  md5: 8035e5b54c08429354d5d64027041cad
-  depends:
-  - libstdcxx >=14
-  - libgcc >=14
-  - __glibc >=2.17,<3.0.a0
-  - libgcc >=14
-  - libsodium >=1.0.20,<1.0.21.0a0
-  - krb5 >=1.21.3,<1.22.0a0
-  license: MPL-2.0
-  license_family: MOZILLA
-  size: 310648
-  timestamp: 1757370847287
-- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zeromq-4.3.5-h888dc83_9.conda
-  sha256: b6f9c130646e5971f6cad708e1eee278f5c7eea3ca97ec2fdd36e7abb764a7b8
-  md5: 26f39dfe38a2a65437c29d69906a0f68
-  depends:
-  - __osx >=11.0
-  - libcxx >=19
-  - libsodium >=1.0.20,<1.0.21.0a0
-  - krb5 >=1.21.3,<1.22.0a0
-  license: MPL-2.0
-  license_family: MOZILLA
-  size: 244772
-  timestamp: 1757371008525
 - conda: https://conda.anaconda.org/conda-forge/win-64/zeromq-4.3.5-h5bddc39_9.conda
   sha256: 690cf749692c8ea556646d1a47b5824ad41b2f6dfd949e4cdb6c44a352fcb1aa
   md5: a6c8f8ee856f7c3c1576e14b86cd8038
@@ -13731,36 +15927,6 @@ packages:
   license_family: MOZILLA
   size: 265212
   timestamp: 1757370864284
-- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.0-pyhcf101f3_1.conda
-  sha256: b4533f7d9efc976511a73ef7d4a2473406d7f4c750884be8e8620b0ce70f4dae
-  md5: 30cd29cb87d819caead4d55184c1d115
-  depends:
-  - python >=3.10
-  - python
-  license: MIT
-  license_family: MIT
-  size: 24194
-  timestamp: 1764460141901
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.2-h25fd6f3_2.conda
-  sha256: 245c9ee8d688e23661b95e3c6dd7272ca936fabc03d423cdb3cdee1bbcf9f2f2
-  md5: c2a01a08fc991620a74b32420e97868a
-  depends:
-  - __glibc >=2.17,<3.0.a0
-  - libzlib 1.3.2 h25fd6f3_2
-  license: Zlib
-  license_family: Other
-  size: 95931
-  timestamp: 1774072620848
-- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zlib-1.3.2-h8088a28_2.conda
-  sha256: 8dd2ac25f0ba714263aac5832d46985648f4bfb9b305b5021d702079badc08d2
-  md5: f1c0bce276210bed45a04949cfe8dc20
-  depends:
-  - __osx >=11.0
-  - libzlib 1.3.2 h8088a28_2
-  license: Zlib
-  license_family: Other
-  size: 81123
-  timestamp: 1774072974535
 - conda: https://conda.anaconda.org/conda-forge/win-64/zlib-1.3.2-hfd05255_2.conda
   sha256: ef408f85f664a4b9c9dac3cb2e36154d9baa15a88984ea800e11060e0f2394a1
   md5: 5187ecf958be3c39110fe691cbd6873e
@@ -13771,29 +15937,11 @@ packages:
   - vc14_runtime >=14.44.35208
   license: Zlib
   license_family: Other
+  run_exports:
+    weak:
+    - libzlib >=1.3.2,<2.0a0
   size: 850351
   timestamp: 1774072891049
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.3.3-hceb46e0_1.conda
-  sha256: ea4e50c465d70236408cb0bfe0115609fd14db1adcd8bd30d8918e0291f8a75f
-  md5: 2aadb0d17215603a82a2a6b0afd9a4cb
-  depends:
-  - __glibc >=2.17,<3.0.a0
-  - libgcc >=14
-  - libstdcxx >=14
-  license: Zlib
-  license_family: Other
-  size: 122618
-  timestamp: 1770167931827
-- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zlib-ng-2.3.3-hed4e4f5_1.conda
-  sha256: a339606a6b224bb230ff3d711e801934f3b3844271df9720165e0353716580d4
-  md5: d99c2a23a31b0172e90f456f580b695e
-  depends:
-  - __osx >=11.0
-  - libcxx >=19
-  license: Zlib
-  license_family: Other
-  size: 94375
-  timestamp: 1770168363685
 - conda: https://conda.anaconda.org/conda-forge/win-64/zlib-ng-2.3.3-h0261ad2_1.conda
   sha256: 71332532332d13b5dbe57074ddcf82ae711bdc132affa5a2982a29ffa06dc234
   md5: 46a21c0a4e65f1a135251fc7c8663f83
@@ -13803,38 +15951,11 @@ packages:
   - vc14_runtime >=14.44.35208
   license: Zlib
   license_family: Other
+  run_exports:
+    weak:
+    - zlib-ng >=2.3.3,<2.4.0a0
   size: 124542
   timestamp: 1770167984883
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zstandard-0.25.0-py313h54dd161_1.conda
-  sha256: e6921de3669e1bbd5d050a3b771b46a887e7f4ffeb1ddd5e4d9fb01062a2f6e9
-  md5: 710d4663806d0f72b2fb414e936223b5
-  depends:
-  - python
-  - cffi >=1.11
-  - zstd >=1.5.7,<1.5.8.0a0
-  - libgcc >=14
-  - __glibc >=2.17,<3.0.a0
-  - python_abi 3.13.* *_cp313
-  - zstd >=1.5.7,<1.6.0a0
-  license: BSD-3-Clause
-  license_family: BSD
-  size: 471496
-  timestamp: 1762512679097
-- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zstandard-0.25.0-py313h9734d34_1.conda
-  sha256: c8525ae1a739db3c9b4f901d08fd7811402cf46b61ddf5d63419a3c533e02071
-  md5: 7ac13a947d4d9f57859993c06faf887b
-  depends:
-  - python
-  - cffi >=1.11
-  - zstd >=1.5.7,<1.5.8.0a0
-  - __osx >=11.0
-  - python 3.13.* *_cp313
-  - zstd >=1.5.7,<1.6.0a0
-  - python_abi 3.13.* *_cp313
-  license: BSD-3-Clause
-  license_family: BSD
-  size: 396449
-  timestamp: 1762512722894
 - conda: https://conda.anaconda.org/conda-forge/win-64/zstandard-0.25.0-py313h5fd188c_1.conda
   sha256: 5f751687a64cf5a6d69ad79aa437f45d6cc388d9e887dcdecff9d3b08cf7fd87
   md5: 46f6f9bb324a58a9b081bbc56ade37f2
@@ -13854,26 +15975,6 @@ packages:
   license_family: BSD
   size: 380854
   timestamp: 1762512720226
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda
-  sha256: 68f0206ca6e98fea941e5717cec780ed2873ffabc0e1ed34428c061e2c6268c7
-  md5: 4a13eeac0b5c8e5b8ab496e6c4ddd829
-  depends:
-  - __glibc >=2.17,<3.0.a0
-  - libzlib >=1.3.1,<2.0a0
-  license: BSD-3-Clause
-  license_family: BSD
-  size: 601375
-  timestamp: 1764777111296
-- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zstd-1.5.7-hbf9d68e_6.conda
-  sha256: 9485ba49e8f47d2b597dd399e88f4802e100851b27c21d7525625b0b4025a5d9
-  md5: ab136e4c34e97f34fb621d2592a393d8
-  depends:
-  - __osx >=11.0
-  - libzlib >=1.3.1,<2.0a0
-  license: BSD-3-Clause
-  license_family: BSD
-  size: 433413
-  timestamp: 1764777166076
 - conda: https://conda.anaconda.org/conda-forge/win-64/zstd-1.5.7-h534d264_6.conda
   sha256: 368d8628424966fd8f9c8018326a9c779e06913dd39e646cf331226acc90e5b2
   md5: 053b84beec00b71ea8ff7a4f84b55207
@@ -13884,5 +15985,8 @@ packages:
   - libzlib >=1.3.1,<2.0a0
   license: BSD-3-Clause
   license_family: BSD
+  run_exports:
+    weak:
+    - zstd >=1.5.7,<1.6.0a0
   size: 388453
   timestamp: 1764777142545
diff --git a/pixi.toml b/pixi.toml
index b48f914..e8864ed 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -1,7 +1,7 @@
 [workspace]
 name = "module_co2stop_cdr"
 authors = ["See AUTHORS file"]
-description = "A module to aggregate CDR potential in Europe into flexible spatial resolutions, using the CO2Stop dataset"
+description = "A module to aggregate CDR potential in Europe into flexible spatial resolutions, using the CO2Stop dataset."
 license = "Apache-2.0"
 readme = "README.md"
 channels = ["conda-forge", "bioconda"]
@@ -9,7 +9,7 @@ platforms = ["win-64", "linux-64", "osx-arm64"]
 homepage = "https://www.modelblocks.org/"
 
 [dependencies]
-clio-tools = ">=2026.03.30"
+clio-tools = ">=2026.06.23"
 conda = ">=25.0.0"
 ipdb = ">=0.13.13"
 ipykernel = ">=6.29.5"
@@ -19,31 +19,50 @@ pytest = ">=8.3.5"
 python = ">=3.12"
 ruff = ">=0.9.9"
 snakefmt = ">=0.10.2"
-snakemake-minimal = ">=8.29.0"
+snakemake-minimal = ">=9.19.0"
 pytz = ">=2026.1.post1"
 
+[feature.module.dependencies]
+cmap = ">=0.7.0"
+curl = ">=8.9.1"
+geopandas = ">=1.0.1"
+ipdb = ">=0.13.13"
+pandas = ">=3.0.0"
+matplotlib = ">=3.10.8"
+numpy = ">=2.4.1"
+pandera = ">=0.28.1"
+pandera-base = ">=0.28.1"
+pandera-geopandas = ">=0.28.1"
+pandera-pandas = ">=0.28.1"
+pyarrow = ">=23.0.0"
+pyproj = ">=3.7.2"
+python = ">=3.13.11"
+pytz = ">=2025.2"
+fiona = ">=1.10.1"
+
+[environments]
+module = { features = ["module"], no-default-feature = true }
+
 [tasks]
 test-integration = {cmd = "pytest tests/integration_test.py"}
 
-[feature.co2stop]
-channels = ["conda-forge"]
-
-[feature.co2stop.dependencies]
-cmap = "0.7.0.*"
-geopandas = "1.0.1.*"
-ipdb = "0.13.13.*"
-pandas = "3.0.0.*"
-matplotlib = "3.10.8.*"
-numpy = "2.4.1.*"
-pandera = "0.28.1.*"
-pandera-base = "0.28.1.*"
-pandera-geopandas = "0.28.1.*"
-pandera-pandas = "0.28.1.*"
-pyarrow = "23.0.0.*"
-pyproj = "3.7.2.*"
-python = "3.13.11.*"
-pytz = "2025.2.*"
-fiona = "1.10.1.*"
 
-[environments]
-co2stop = { features = ["co2stop"], no-default-feature = true }
+[tasks.export-snakemake-env]
+description = "Export one Pixi environment as Snakemake-compatible conda files"
+args = ["env", { arg = "outdir", default = "workflow/envs" }]
+depends-on = [
+  { task = "_export-snakemake-pin", args = ["{{ env }}", "win-64", "{{ outdir }}"] },
+  { task = "_export-snakemake-pin", args = ["{{ env }}", "linux-64", "{{ outdir }}"] },
+  { task = "_export-snakemake-pin", args = ["{{ env }}", "osx-arm64", "{{ outdir }}"] },
+]
+cmd = "pixi workspace export conda-environment --environment '{{ env }}' '{{ outdir }}/{{ env }}.yaml'"
+
+[tasks._export-snakemake-pin]
+description = "Export one Pixi environment/platform as a Snakemake-compatible pin file"
+args = ["env", "platform", { arg = "outdir", default = "workflow/envs" }]
+cmd = """
+set -e
+pixi workspace export conda-explicit-spec --environment '{{ env }}' --platform '{{ platform }}' '{{ outdir }}'
+mv '{{ outdir }}/{{ env }}_{{ platform }}_conda_spec.txt' '{{ outdir }}/{{ env }}.{{ platform }}.pin.txt'
+"""
+
diff --git a/tests/conftest.py b/tests/conftest.py
index fea4a64..1605812 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -11,6 +11,12 @@
 TEST_FILES = "https://zenodo.org/records/18153129/files/test_suite.zip?download=1"
 
 
+@pytest.fixture(scope="module")
+def module_path():
+    """Parent directory of the project."""
+    return Path(__file__).parent.parent
+
+
 @pytest.fixture(scope="session")
 def user_path() -> Path:
     """Download and unzip test files."""
@@ -25,3 +31,20 @@ def user_path() -> Path:
         with zipfile.ZipFile(test_zip, "r") as zfile:
             zfile.extractall(dir)
     return dir / "user"
+
+
+@pytest.fixture(scope="module")
+def integration_path(user_path: Path, module_path: Path):
+    """Ensures the minimal integration test is ready."""
+    integration_dir = Path(module_path / "tests/integration")
+    if integration_dir.exists():
+        shutil.rmtree(
+            integration_dir / "results/", ignore_errors=True
+        )  # clean everything
+    user_integ_dir = integration_dir / "resources/inputs/"
+    files_to_copy = ["BALK/shapes.parquet"]
+    for file in files_to_copy:
+        destination_file = Path(user_integ_dir / file)
+        destination_file.parent.mkdir(parents=True, exist_ok=True)
+        shutil.copy(user_path / file, destination_file)
+    return integration_dir
diff --git a/tests/integration/Snakefile b/tests/integration/Snakefile
index c0a788c..40a59bd 100644
--- a/tests/integration/Snakefile
+++ b/tests/integration/Snakefile
@@ -18,9 +18,9 @@ module module_co2stop_cdr:
         cdr_group="results/outputs/{shapes}/{scenario}/{cdr_group}.parquet",
         total_aggregate="results/outputs/{shapes}/{scenario}/totals.parquet",
         # Redirect module intermediate files
-        logs="resources/co2stop_cdr/logs",
-        resources="resources/co2stop_cdr/resources",
-        results="resources/co2stop_cdr/results",
+        logs="resources/module/logs",
+        resources="resources/module/resources",
+        results="resources/module/results",
     snakefile:
         "../../workflow/Snakefile"
     config:
diff --git a/tests/integration_test.py b/tests/integration_test.py
index 16548e9..07e72e5 100644
--- a/tests/integration_test.py
+++ b/tests/integration_test.py
@@ -4,8 +4,8 @@
 Contents may be updated in future template updates.
 """
 
-import shutil
 import subprocess
+import tomllib
 from pathlib import Path
 
 import pytest
@@ -13,26 +13,34 @@
 
 
 @pytest.fixture(scope="module")
-def module_path():
-    """Parent directory of the project."""
-    return Path(__file__).parent.parent
+def pixi_platforms(module_path) -> list[str]:
+    """Pixi platforms defined for this project."""
+    with (module_path / "pixi.toml").open("rb") as pixi_config:
+        return tomllib.load(pixi_config)["workspace"]["platforms"]
 
 
-@pytest.fixture(scope="module")
-def integration_path(user_path: Path, module_path: Path):
-    """Ensures the minimal integration test is ready."""
-    integration_dir = Path(module_path / "tests/integration")
-    if integration_dir.exists():
-        shutil.rmtree(
-            integration_dir / "results/", ignore_errors=True
-        )  # clean everything
-    user_integ_dir = integration_dir / "resources/inputs/"
-    files_to_copy = ["BALK/shapes.parquet"]
-    for file in files_to_copy:
-        destination_file = Path(user_integ_dir / file)
-        destination_file.parent.mkdir(parents=True, exist_ok=True)
-        shutil.copy(user_path / file, destination_file)
-    return integration_dir
+def test_snakemake_environments(module_path, pixi_platforms, tmp_path):
+    """All Snakemake environment files should be based on pixi counterparts."""
+    env_dir = module_path / "workflow/envs"
+    env_files = sorted(env_dir.glob("*.yaml"))
+    assert env_files, f"No conda environments found in {module_path}."
+
+    for env_file in env_files:
+        env_name = env_file.stem
+
+        output_dir = tmp_path / env_name
+        subprocess.run(
+            ["pixi", "run", "export-snakemake-env", env_name, str(output_dir)],
+            check=True,
+            cwd=module_path,
+        )
+
+        generated_yaml = output_dir / env_file.name
+        assert generated_yaml.read_text() == env_file.read_text()
+
+        for platform in pixi_platforms:
+            pin_file = env_dir / f"{env_name}.{platform}.pin.txt"
+            assert pin_file.exists(), f"{env_name} has no conda pins for {platform}"
 
 
 def test_interface_file(module_path):
@@ -43,15 +51,18 @@ def test_interface_file(module_path):
 @pytest.mark.parametrize(
     "file",
     [
-        "CITATION.cff",
         "AUTHORS",
+        "CITATION.cff",
         "INTERFACE.yaml",
         "LICENSE",
+        "README.md",
+        "config/config.yaml",
+        "workflow/internal/config.schema.yaml",
         "tests/integration/Snakefile",
     ],
 )
 def test_standard_file_existance(module_path, file):
-    """Check that a minimal set of files used for clio automatic docs are present."""
+    """Check that a minimal set of files used for documentation are present."""
     assert Path(module_path / file).exists()
 
 
@@ -60,7 +71,7 @@ def test_snakemake_all_failure(module_path):
     process = subprocess.run(
         "snakemake --cores 1", shell=True, cwd=module_path, capture_output=True
     )
-    assert "INVALID (missing locally)" in str(process.stderr)
+    assert "INVALID" in str(process.stderr)
 
 
 def test_snakemake_integration_testing(integration_path):
diff --git a/workflow/Snakefile b/workflow/Snakefile
index 1b9839f..1b5cf07 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -49,7 +49,7 @@ rule all:
     log:
         stderr="<logs>/all.stderr",
     conda:
-        "envs/shell.yaml"
+        "envs/module.yaml"
     message:
         "ERROR: Invalid `rule all:` call"
     shell:
diff --git a/workflow/envs/co2stop.yaml b/workflow/envs/co2stop.yaml
deleted file mode 100644
index 9795486..0000000
--- a/workflow/envs/co2stop.yaml
+++ /dev/null
@@ -1,20 +0,0 @@
-name: co2stop
-channels:
-- conda-forge
-- nodefaults
-dependencies:
-- cmap 0.7.0.*
-- geopandas 1.0.1.*
-- ipdb 0.13.13.*
-- pandas 3.0.0.*
-- matplotlib 3.10.8.*
-- numpy 2.4.1.*
-- pandera 0.28.1.*
-- pandera-base 0.28.1.*
-- pandera-geopandas 0.28.1.*
-- pandera-pandas 0.28.1.*
-- pyarrow 23.0.0.*
-- pyproj 3.7.2.*
-- python 3.13.11.*
-- pytz 2025.2.*
-- fiona 1.10.1.*
diff --git a/workflow/envs/co2stop.linux-64.pin.txt b/workflow/envs/module.linux-64.pin.txt
similarity index 73%
rename from workflow/envs/co2stop.linux-64.pin.txt
rename to workflow/envs/module.linux-64.pin.txt
index 92eccb4..2664dce 100644
--- a/workflow/envs/co2stop.linux-64.pin.txt
+++ b/workflow/envs/module.linux-64.pin.txt
@@ -3,53 +3,52 @@
 @EXPLICIT
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-https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_18.conda#239c5e9546c38a1e884d69effcf4c882
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_19.conda#faac990cb7aedc7f3a2224f2c9b0c26c
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda#a9f577daf3de00bca7c3c76c0ecbd1de
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_18.conda#0aa00f03f9e39fb9876085dee11a85d4
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_19.conda#57736f29cc2b0ec0b6c2952d3f101b6a
 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h366c992_103.conda#cffd3bdd58090148f4cfcd831f4b26ab
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.6-hdb14827_0.conda#fc21868a1a5aacc937e7a18747acb8a5
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-https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.19.0-hcf29cc6_0.conda#d50608c443a30c341c24277d28290f76
+https://conda.anaconda.org/conda-forge/linux-64/krb5-1.22.2-hbde042b_1.conda#54157a1c8c0bb70f62dd0b17fba7e7f2
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-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-15.2.0-hdf11a46_18.conda#6235adb93d064ecdf3d44faee6f468de
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-15.2.0-hdf11a46_19.conda#e5ce228e579726c07255dbf90dc62101
 https://conda.anaconda.org/conda-forge/linux-64/libcrc32c-1.1.2-h9c3ff4c_0.tar.bz2#c965a5aa0d5c1c37ffc62dff36e28400
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@@ -58,12 +57,13 @@ https://conda.anaconda.org/conda-forge/linux-64/libbrotlidec-1.2.0-hb03c661_1.co
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-https://conda.anaconda.org/conda-forge/linux-64/libxml2-16-2.15.2-hca6bf5a_0.conda#f3bc152cb4f86babe30f3a4bf0dbef69
-https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.15.2-he237659_0.conda#e49238a1609f9a4a844b09d9926f2c3d
+https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h33c6efd_0.conda#c80d8a3b84358cb967fa81e7075fbc8a
+https://conda.anaconda.org/conda-forge/linux-64/libxml2-16-2.15.3-hca6bf5a_0.conda#e79d2c2f24b027aa8d5ab1b1ba3061e7
+https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.15.3-h49c6c72_0.conda#995d8c8bad2a3cc8db14675a153dec2b
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-https://conda.anaconda.org/conda-forge/linux-64/azure-storage-files-datalake-cpp-12.14.0-h52c5a47_1.conda#6d10339800840562b7dad7775f5d2c16
+https://conda.anaconda.org/conda-forge/linux-64/azure-storage-common-cpp-12.13.0-ha7a2c86_0.conda#a7e8cca395e0a1616b389749580b7804
+https://conda.anaconda.org/conda-forge/linux-64/azure-storage-blobs-cpp-12.16.0-hf824e48_2.conda#315c1c09f02a1efeb1b4d3dbcd2aa26a
+https://conda.anaconda.org/conda-forge/linux-64/azure-storage-files-datalake-cpp-12.14.0-h539c000_2.conda#245b61f9baef23f8f6cf04ccda928521
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@@ -83,7 +83,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libarrow-23.0.0-h2603568_3_cpu.c
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@@ -92,24 +92,24 @@ https://conda.anaconda.org/conda-forge/linux-64/pyarrow-23.0.0-py313h78bf25f_0.c
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diff --git a/workflow/envs/co2stop.osx-arm64.pin.txt b/workflow/envs/module.osx-arm64.pin.txt
similarity index 75%
rename from workflow/envs/co2stop.osx-arm64.pin.txt
rename to workflow/envs/module.osx-arm64.pin.txt
index 18a8506..803b1a8 100644
--- a/workflow/envs/co2stop.osx-arm64.pin.txt
+++ b/workflow/envs/module.osx-arm64.pin.txt
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diff --git a/workflow/envs/co2stop.win-64.pin.txt b/workflow/envs/module.win-64.pin.txt
similarity index 69%
rename from workflow/envs/co2stop.win-64.pin.txt
rename to workflow/envs/module.win-64.pin.txt
index dc7116e..6c3d9cf 100644
--- a/workflow/envs/co2stop.win-64.pin.txt
+++ b/workflow/envs/module.win-64.pin.txt
@@ -2,20 +2,20 @@
 # platform: win-64
 @EXPLICIT
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-https://conda.anaconda.org/conda-forge/noarch/wcwidth-0.6.0-pyhd8ed1ab_0.conda#c3197f8c0d5b955c904616b716aca093
+https://conda.anaconda.org/conda-forge/win-64/psutil-7.2.2-py313h5fd188c_0.conda#761b299a6289c77459defea3563f8fc0
+https://conda.anaconda.org/conda-forge/noarch/wcwidth-0.8.1-pyhd8ed1ab_0.conda#19c961dd9cab6c3e13cd195f0176dbfa
 https://conda.anaconda.org/conda-forge/noarch/prompt-toolkit-3.0.52-pyha770c72_0.conda#edb16f14d920fb3faf17f5ce582942d6
-https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.2.1-pyhd8ed1ab_0.conda#00e120ce3e40bad7bfc78861ce3c4a25
-https://conda.anaconda.org/conda-forge/noarch/parso-0.8.6-pyhcf101f3_0.conda#97c1ce2fffa1209e7afb432810ec6e12
-https://conda.anaconda.org/conda-forge/noarch/jedi-0.19.2-pyhd8ed1ab_1.conda#a4f4c5dc9b80bc50e0d3dc4e6e8f1bd9
+https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.2.2-pyhd8ed1ab_0.conda#9acc1c385be401d533ff70ef5b50dae6
+https://conda.anaconda.org/conda-forge/noarch/parso-0.8.7-pyhcf101f3_0.conda#39894c952938276405a1bd30e4ce2caf
+https://conda.anaconda.org/conda-forge/noarch/jedi-0.20.0-pyhcf101f3_0.conda#c2b3d37aa1411031126036ee76a8a861
 https://conda.anaconda.org/conda-forge/noarch/ipython_pygments_lexers-1.1.1-pyhd8ed1ab_0.conda#bd80ba060603cc228d9d81c257093119
-https://conda.anaconda.org/conda-forge/noarch/decorator-5.2.1-pyhd8ed1ab_0.conda#9ce473d1d1be1cc3810856a48b3fab32
+https://conda.anaconda.org/conda-forge/noarch/decorator-5.3.1-pyhd8ed1ab_0.conda#61dcf784d59ef0bd62c57d982b154ace
 https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_1.conda#962b9857ee8e7018c22f2776ffa0b2d7
-https://conda.anaconda.org/conda-forge/noarch/ipython-9.12.0-pyhccfa634_0.conda#3734e3b6618ea6e04ad08678d8ed7a45
+https://conda.anaconda.org/conda-forge/noarch/ipython-9.14.1-pyhe2676ad_0.conda#bf12187c2d1ef0bb63df01ace31ff26b
 https://conda.anaconda.org/conda-forge/noarch/ipdb-0.13.13-pyhd8ed1ab_1.conda#044c5249ad8ea18a414d07baa1f369ea
-https://conda.anaconda.org/conda-forge/noarch/click-8.3.1-pyha7b4d00_1.conda#6cd3ccc98bacfcc92b2bd7f236f01a7e
+https://conda.anaconda.org/conda-forge/noarch/click-8.4.1-pyh6dadd2b_0.conda#f73f35eedcd8e89d6c4407df15101233
 https://conda.anaconda.org/conda-forge/noarch/cligj-0.7.2-pyhd8ed1ab_2.conda#55c7804f428719241a90b152016085a1
 https://conda.anaconda.org/conda-forge/noarch/click-plugins-1.1.1.2-pyhd8ed1ab_0.conda#e9b05deb91c013e5224672a4ba9cf8d1
 https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda#c6b0543676ecb1fb2d7643941fe375f2
 https://conda.anaconda.org/conda-forge/win-64/fiona-1.10.1-py313h8b19803_6.conda#c048daef67f2a62c12200e6c4f1ad688
+https://conda.anaconda.org/conda-forge/win-64/curl-8.21.0-h8206538_0.conda#b09f232e463d78e4cc0bec233007441b
 https://conda.anaconda.org/conda-forge/noarch/cmap-0.7.0-pyhd8ed1ab_0.conda#c723262cfa0dfa2d2f12e4969a993f0f
diff --git a/workflow/envs/module.yaml b/workflow/envs/module.yaml
new file mode 100644
index 0000000..296edca
--- /dev/null
+++ b/workflow/envs/module.yaml
@@ -0,0 +1,22 @@
+name: module
+channels:
+- conda-forge
+- bioconda
+- nodefaults
+dependencies:
+- cmap >=0.7.0
+- curl >=8.9.1
+- geopandas >=1.0.1
+- ipdb >=0.13.13
+- pandas >=3.0.0
+- matplotlib >=3.10.8
+- numpy >=2.4.1
+- pandera >=0.28.1
+- pandera-base >=0.28.1
+- pandera-geopandas >=0.28.1
+- pandera-pandas >=0.28.1
+- pyarrow >=23.0.0
+- pyproj >=3.7.2
+- python >=3.13.11
+- pytz >=2025.2
+- fiona >=1.10.1
diff --git a/workflow/envs/shell.yaml b/workflow/envs/shell.yaml
deleted file mode 100644
index e4b351d..0000000
--- a/workflow/envs/shell.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-name: shell
-channels:
-  - conda-forge
-  - nodefaults
-dependencies:
-  - curl=8.9.1
diff --git a/workflow/rules/aggregate.smk b/workflow/rules/aggregate.smk
index 67b078e..a965f58 100644
--- a/workflow/rules/aggregate.smk
+++ b/workflow/rules/aggregate.smk
@@ -20,7 +20,7 @@ rule aggregate_co2stop:
         scenario="|".join(["low", "medium", "high"]),
         cdr_group="|".join(CDR_GROUP),
     conda:
-        "../envs/co2stop.yaml"
+        "../envs/module.yaml"
     params:
         bounds_mtco2=lambda wc: config["imputation"]["aggregated"][wc.cdr_group][
             "bounds_mtco2"
@@ -54,7 +54,7 @@ rule aggregate_totals:
     wildcard_constraints:
         scenario="|".join(["low", "medium", "high"]),
     conda:
-        "../envs/co2stop.yaml"
+        "../envs/module.yaml"
     params:
         proj_crs=config["crs"]["projected"],
     message:
diff --git a/workflow/rules/automatic.smk b/workflow/rules/automatic.smk
index cf3496d..375674d 100644
--- a/workflow/rules/automatic.smk
+++ b/workflow/rules/automatic.smk
@@ -7,7 +7,7 @@ rule download_co2stop:
     log:
         "<logs>/download_co2stop.log",
     conda:
-        "../envs/shell.yaml"
+        "../envs/module.yaml"
     params:
         url=internal["resources"]["automatic"]["co2stop"],
     message:
@@ -28,7 +28,7 @@ rule unzip_co2stop:
     log:
         "<logs>/automatic/unzip_co2stop.log",
     conda:
-        "../envs/co2stop.yaml"
+        "../envs/module.yaml"
     params:
         storage_data="CO2Stop_DataInterrogationSystem/Hydrocarbon_Storage_Units.csv",
         storage_map="CO2Stop_Polygons Data/StorageUnits_March13.kml",
diff --git a/workflow/rules/prepare.smk b/workflow/rules/prepare.smk
index 13ac0c1..e772307 100644
--- a/workflow/rules/prepare.smk
+++ b/workflow/rules/prepare.smk
@@ -25,7 +25,7 @@ rule prepare_co2stop_storage_units:
     log:
         "<logs>/storage_units/aquifer/prepare_co2stop.log",
     conda:
-        "../envs/co2stop.yaml"
+        "../envs/module.yaml"
     params:
         cdr_group="aquifer",
         cdr_group_config=lambda wc: config["imputation"]["co2stop"]["aquifer"],
@@ -61,7 +61,7 @@ rule prepare_co2stop_traps:
     wildcard_constraints:
         cdr_group="|".join(CDR_GROUP),
     conda:
-        "../envs/co2stop.yaml"
+        "../envs/module.yaml"
     params:
         cdr_group=lambda wc: wc.cdr_group,
         cdr_group_config=lambda wc: config["imputation"]["co2stop"][wc.cdr_group],

From a4a192fdddf4ff5601db47ae5770dec759133e4c Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 24 Jun 2026 18:21:27 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 pixi.toml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pixi.toml b/pixi.toml
index e8864ed..cd25d8e 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -65,4 +65,3 @@ set -e
 pixi workspace export conda-explicit-spec --environment '{{ env }}' --platform '{{ platform }}' '{{ outdir }}'
 mv '{{ outdir }}/{{ env }}_{{ platform }}_conda_spec.txt' '{{ outdir }}/{{ env }}.{{ platform }}.pin.txt'
 """
-