Merge pull request #311 from softwarepub/feature/fix-small-issues-before-090

Small fixes to prepare v0.9.0

Author: nheeb

.github/workflows/cffconvert.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out a copy of the repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Check whether the citation metadata from CITATION.cff is valid
         uses: citation-file-format/cffconvert-github-action@2.0.0

.github/workflows/hermes-zenodo.yml

@@ -38,8 +38,8 @@ jobs:
       pull-requests: write # Postprocessing should be able to create a pull request with changes
 
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.10'
       - run: pip install hermes hermes-plugin-python
@@ -61,7 +61,7 @@ jobs:
 
           # Explicitly add to-be-curated metadata (which is ignored via .gitignore!)
           git add -f .hermes/curate
-      - uses: peter-evans/create-pull-request@v5
+      - uses: peter-evans/create-pull-request@v7
         with:
           base: hermes/curate-${{ env.SHORT_SHA }}
           branch: hermes/curate-result-${{ env.SHORT_SHA }}
@@ -82,8 +82,8 @@ jobs:
       pull-requests: write # Postprocessing should be able to create a pull request with changes
 
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.10'
       - run: pip install hermes
@@ -115,7 +115,7 @@ jobs:
       # Note 2: The create-pull-request action will NOT inherit the commits we did in the previous job. It will only look at the
       #         changes within this local workspace we did *now*.
       - run: echo "TARGET_BRANCH=$(cat .hermes/curate/target_branch)" >> "$GITHUB_ENV"
-      - uses: peter-evans/create-pull-request@v5
+      - uses: peter-evans/create-pull-request@v7
         with:
           branch: hermes/post-${{ github.run_id }}
           base: ${{ env.TARGET_BRANCH }}
@@ -143,7 +143,7 @@ jobs:
       pull-requests: write # Postprocessing should be able to create a pull request with changes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       # Delete all the curation branches
       - run: |
           for BRANCH in $(git ls-remote origin 'refs/heads/hermes/curate-*' | cut -f2 | cut -d'/' -f'3-'); do

.github/workflows/release.yml

@@ -22,7 +22,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: "3.10"
     - name: Install pypa/build
@@ -34,7 +34,7 @@ jobs:
     - name: Build a binary wheel and a source tarball
       run: python3 -m build
     - name: Store the distribution packages
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: python-package-distributions
         path: dist/
@@ -54,7 +54,7 @@ jobs:
 
     steps:
     - name: Download all the dists
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: python-package-distributions
         path: dist/

.github/workflows/tests.yml

@@ -18,24 +18,22 @@ jobs:
         python-version: ["3.10"]  # Ignore Python < 3.10, they are unsupported
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install flake8 pytest
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+          python -m pip install --upgrade pip poetry
+          poetry install
       - name: Lint with flake8
         run: |
           # stop the build if there are Python syntax errors or undefined names
-          flake8 ./test/ ./src/ --count --select=E9,F63,F7,F82 --show-source --statistics
+          poetry run flake8 ./test/ ./src/ --count --select=E9,F63,F7,F82 --show-source --statistics
           # Stop build on errors
-          flake8 ./test/ ./src/ --count --statistics
+          poetry run flake8 ./test/ ./src/ --count --statistics
       - name: Test with pytest
         run: |
-          pip install -e .
-          pip install requests-mock
-          pytest ./test/
+          poetry install
+          poetry run pytest

CITATION.cff

@@ -29,15 +29,10 @@ authors:
     email: stephan.druskat@dlr.de
     affiliation: German Aerospace Center (DLR)
     orcid: 'https://orcid.org/0000-0003-4925-7248'
-  - given-names: Jeffrey
-    family-names: Kelling
-    email: j.kelling@hzdr.de
-    affiliation: Helmholtz-Zentrum Dresden-Rossendorf (HZDR)
-    orcid: 'https://orcid.org/0000-0003-1761-2591'
   - given-names: Oliver
     family-names: Bertuch
     email: o.bertuch@fz-juelich.de
-    affiliation: Forschungszentrum Jülich GmbH (FZJ)
+    affiliation: Forschungszentrum Jülich
     orcid: 'https://orcid.org/0000-0002-2702-3419'
   - given-names: Oliver
     family-names: Knodel
@@ -54,6 +49,11 @@ authors:
     email: sophie.kernchen@dlr.de
     affiliation: German Aerospace Center (DLR)
     orcid: 'https://orcid.org/0009-0005-4430-6743'
+  - given-names: Nitai
+    family-names: Heeb
+    email: n.heeb@fz-juelich.de
+    affiliation: Forschungszentrum Jülich
+    orcid: 'https://orcid.org/0009-0001-8382-4923'
 identifiers:
   - type: doi
     value: 10.5281/zenodo.13221384

GOVERNANCE.md

@@ -1,81 +1,84 @@
-<!--
-SPDX-FileCopyrightText: 2024 German Aerospace Center (DLR)
-SPDX-FileContributor: Stephan Druskat
-
-SPDX-License-Identifier: CC-BY-SA-4.0
--->
-
-## Governance
-
-The HERMES project employs a lightweight governance model.
-
-All decisions are made by the [HERMES Steering Group](#hermes-steering-group) 
-together with the maintainer(s) of the repositories affected by the decision.
-
-Decisions that adhere to a single [repository in the scope of the HERMES project](#hermes-project-repositories)
-are made by *lazy consensus*: 
-
-1. The maintainer of the repository makes a decision and notifies the HERMES Steering Group
-(using `@softwarepub/hermes-steering-group` mention).
-2. If no members of the Steering Group veto the decision within the decision period of one week (168 hours),
-the decision becomes effective and can be acted upon. 
-The maintainer and any member of the Steering Group can ask for a longer decision period, 
-which must be granted. 
-During this period, the steering committee should meet to discuss the decision.
-3. If one or more members of the Steering Group veto the decision, 
-the decision is discussed until consensus is reached.
-
-Decisions that adhere to more than one [repository in the scope of the HERMES project](#hermes-project-repositories)
-must be based on full consensus within the Steering Group. 
-
-
-### HERMES project repositories
-
-The following are the repositories that are governed by the Steering Group. 
-
-- <https://github.com/softwarepub/hermes> (Maintainer: Stephan Druskat)
-- <https://github.com/softwarepub/ci-templates> (Maintainer: Oliver Bertuch)
-- <https://github.com/softwarepub/hermes-plugin-git> (Maintainer: Sophie Kernchen)
-- <https://github.com/softwarepub/hermes-plugin-python> (Maintainer: Michael Meinel)
-- <https://github.com/softwarepub/showcase> (Maintainer: Oliver Bertuch)
-- <https://github.com/softwarepub/schema.software-metadata.pub> (Maintainer: Michael Meinel)
-- <https://github.com/softwarepub/github-action> (Maintainer: Oliver Bertuch)
-- <https://github.com/softwarepub/concept-paper> (Maintainer: Stephan Druskat)
-
-New repositories may be added to, 
-and existing repositories may be removed from, 
-the project by the [Steering Group](#hermes-steering-group)
-by updating the above list.
-Any update needs lazy consensus [as defined above](#governance) from all members of the Steering Group.
-
-### HERMES Steering Group
-
-The HERMES Steering Group has three members, 
-each of whom represents one of the three Helmholtz centers 
-who were funded under the original Helmholtz Metadata Collaboration project (ZT-I-PF-3-006), i.e.,
-German Aerospace Center (DLR), 
-Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 
-Forschungszentrum Jülich (FZJ).
-
-Currently the Steering Group consists of:
-
-- Stephan Druskat (DLR), stephan.druskat@dlr.de
-- David Pape (HZDR), d.pape@hzdr.de
-- Nitai Heeb (FZJ), n.heeb@fz-juelich.de
-
-
-Whenever a member of the Steering Group wants to step down,
-they are asked to nominate a successor.
-If no successor is named,
-the two remaining members seek a successor affiliated with the Helmholtz center of the leaving member.
-New members of the Steering Group join if neither of the other two members disagrees with the decision to join. 
-
-### HERMES repository maintainers
-
-Each [repository in the scope of the HERMES project](#hermes-project-repositories) should have one maintainer at all times.
-The Steering Group appoints the maintainer for this repository in agreement with the appointed person.
-Whenever a maintainer wants to step down,
-they are asked to nominate a successor.
-If no successor is named,
-the Steering Group seeks a successor.
-One member of the Steering Group steps in as interim maintainer until a successor is found.
+<!--
+SPDX-FileCopyrightText: 2024 German Aerospace Center (DLR)
+SPDX-FileContributor: Stephan Druskat
+
+SPDX-License-Identifier: CC-BY-SA-4.0
+-->
+
+## Governance
+
+The HERMES project employs a lightweight governance model.
+
+All decisions are made by the [HERMES Steering Group](#hermes-steering-group) 
+together with the maintainer(s) of the repositories affected by the decision.
+
+Decisions that adhere to a single [repository in the scope of the HERMES project](#hermes-project-repositories)
+are made by *lazy consensus*: 
+
+1. The maintainer of the repository makes a decision and notifies the HERMES Steering Group
+(using `@softwarepub/hermes-steering-group` mention).
+2. If no members of the Steering Group veto the decision within the decision period of one week (168 hours),
+the decision becomes effective and can be acted upon. 
+The maintainer and any member of the Steering Group can ask for a longer decision period, 
+which must be granted. 
+During this period, the steering committee should meet to discuss the decision.
+3. If one or more members of the Steering Group veto the decision, 
+the decision is discussed until consensus is reached.
+
+Decisions that adhere to more than one [repository in the scope of the HERMES project](#hermes-project-repositories)
+must be based on full consensus within the Steering Group. 
+
+
+### HERMES project repositories
+
+The following are the repositories that are governed by the Steering Group. 
+
+- <https://github.com/softwarepub/hermes> (Maintainer: Stephan Druskat)
+- <https://github.com/softwarepub/ci-templates> (Maintainer: Oliver Bertuch)
+- <https://github.com/softwarepub/hermes-plugin-git> (Maintainer: Sophie Kernchen)
+- <https://github.com/softwarepub/hermes-plugin-python> (Maintainer: Michael Meinel)
+- <https://github.com/softwarepub/showcase> (Maintainer: Oliver Bertuch)
+- <https://github.com/softwarepub/schema.software-metadata.pub> (Maintainer: Michael Meinel)
+- <https://github.com/softwarepub/github-action> (Maintainer: Oliver Bertuch)
+- <https://github.com/softwarepub/concept-paper> (Maintainer: Stephan Druskat)
+
+New repositories may be added to, 
+and existing repositories may be removed from, 
+the project by the [Steering Group](#hermes-steering-group)
+by updating the above list.
+Any update needs lazy consensus [as defined above](#governance) from all members of the Steering Group.
+
+### HERMES Steering Group
+
+The HERMES Steering Group has three members, 
+each of whom represents one of the three Helmholtz centers 
+who were funded under the original Helmholtz Metadata Collaboration project (ZT-I-PF-3-006), i.e.,
+German Aerospace Center (DLR), 
+Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 
+Forschungszentrum Jülich (FZJ).
+
+Currently, the Steering Group consists of:
+
+- Stephan Druskat (DLR), stephan.druskat@dlr.de
+- David Pape (HZDR), d.pape@hzdr.de
+- Nitai Heeb (FZJ), n.heeb@fz-juelich.de
+
+
+Whenever a member of the Steering Group wants to step down,
+they are asked to nominate a successor.
+If no successor is named,
+the two remaining members seek a successor affiliated with the Helmholtz center of the leaving member.
+New members of the Steering Group join if neither of the other two members disagrees with the decision to join. 
+
+### HERMES repository maintainers
+
+Each [repository in the scope of the HERMES project](#hermes-project-repositories) should have one maintainer at all times.
+The Steering Group appoints the maintainer for this repository in agreement with the appointed person.
+Whenever a maintainer wants to step down,
+they are asked to nominate a successor.
+If no successor is named,
+the Steering Group seeks a successor.
+One member of the Steering Group steps in as interim maintainer until a successor is found.
+
+In addition, all contributors with write access to repositories and regular activities should be added as "authors" to project and build system metadata in alphabetical order.
+They may also qualify for scholarly authorship, which is managed in citation metadata as necessary and may be ordered by other criteria.

docs/source/conf.py

@@ -22,21 +22,58 @@
 #
 import os
 import sys
+import toml
+
 sys.path.insert(0, os.path.abspath('../../src'))
 sys.path.append(os.path.abspath('_ext'))
 
+def read_from_pyproject(file_path="../../pyproject.toml"):
+    """
+    Reads the metadata from the pyproject.toml file.
+
+    :param file_path: Path to the pyproject.toml file (default: "pyproject.toml")
+    :return: A list of authors or a message if no authors are found.
+    """
+    try:
+        # Load the pyproject.toml file
+        data = toml.load(file_path)
+
+        # Navigate to the authors metadata
+        metadata = data.get("tool", {}).get("poetry", {})
+        if not metadata:
+            return "No metadata found in pyproject.toml"
+        return metadata
+    except FileNotFoundError:
+        return f"The file {file_path} was not found."
+    except toml.TomlDecodeError:
+        return f"Failed to parse {file_path}. Ensure it is a valid TOML file."
+    except Exception as e:
+        return f"An unexpected error occurred: {e}"
+
+def read_authors_from_pyproject():
+    metadata = read_from_pyproject()
+    authors = metadata.get("authors", [])
+    if not authors:
+        return "No authors metadata found in pyproject.toml"
+    # Convert the list of authors to a comma-separated string
+    return ", ".join([a.split(" <")[0] for a in authors])
+
+def read_version_from_pyproject():
+    metadata = read_from_pyproject()
+    version = metadata.get("version", "")
+    if not version:
+        return "No version metadata found in pyproject.toml"
+    return version
+
 
 # -- Project information -----------------------------------------------------
 
 project = 'HERMES Workflow'
-copyright = '2024, HERMES project'
-author = 'Oliver Bertuch, Stephan Druskat, Guido Juckeland, Jeffrey Kelling, ' + \
-         'Oliver Knodel, Michael Meinel, Tobias Schlauch, Sophie Kernchen, ' + \
-         'David Pape'
-
+copyright = '2025 by Forschungszentrum Jülich (FZJ), German Aerospace Center (DLR) and Helmholtz-Zentrum Dresden-Rossendorf (HZDR)'
+author = read_authors_from_pyproject()
 
 # The full version, including alpha/beta/rc tags
-release = '2024-01-11'
+release = read_version_from_pyproject()
 
 
 # -- General configuration ---------------------------------------------------