Merge branch 'develop'

.github/ISSUE_TEMPLATE/add-plugin-to-marketplace.yml

@@ -0,0 +1,76 @@
+# SPDX-FileCopyrightText: 2024 Helmholtz-Zentrum Dresden-Rossendorf
+# SPDX-License-Identifier: CC-BY-SA-4.0
+# SPDX-FileContributor: David Pape
+
+name: "Add Plugin to Marketplace"
+description: "I want to add a plugin to the Hermes plugin marketplace."
+title: "[New Plugin]: "
+labels: ["documentation"]
+
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thank you for building a plugin for Hermes and sharing it with the community!
+
+        The [Hermes plugin marketplace](https://hermes.software-metadata.pub#plugins) is a curated list of plugins on our website that allows you to share plugins that you developed, and others to find them.
+
+        Via this issue template, you can send us the required information to add your plugin to the marketplace. Alternatively, you may file a pull request, adding the plugin to [`plugins.json`](https://github.com/softwarepub/hermes/tree/develop/docs/source/plugins.json) yourself.
+
+  - id: "name"
+    type: "input"
+    attributes:
+      label: "Name"
+      description: "The name of the plugin"
+      placeholder: "Foobar Harvesting and Quux Deposit Plugin"
+    validations:
+      required: true
+
+  - id: "author"
+    type: "input"
+    attributes:
+      label: "Author"
+      description: "The author of the plugin, usually a team or organization"
+      placeholder: "Team Quux at Fizzbuzz Institute"
+
+  - id: "description"
+    type: "textarea"
+    attributes:
+      label: "Description"
+      description: "A short description of your plugin"
+      placeholder: "Plugin for harvesting foobar files and uploading deposits to quux repo."
+
+  - id: "steps"
+    type: "dropdown"
+    attributes:
+      label: "Steps"
+      description: "Steps of the Hermes workflow targeted by your plugin"
+      multiple: true
+      options: ["harvest", "process", "curate", "deposit", "postprocess"]
+
+  - id: "harvested-files"
+    type: "input"
+    attributes:
+      label: "Harvested files"
+      description: "The types of files your plugin harvests (if it is a harvest plugin)"
+      placeholder: "foobar, foobar.yml, foobar.json"
+
+  - id: "repository-url"
+    type: "input"
+    attributes:
+      label: "Repository"
+      description: "The link to the repository where users can find and inspect the source code of your plugin"
+      placeholder: "https://git.example.com/quux/hermes-plugin-quux"
+
+  - id: "pypi-url"
+    type: "input"
+    attributes:
+      label: "PyPI URL"
+      description: "The link to your project on PyPI"
+      placeholder: "https://pypi.org/project/hermes-plugin-quux/"
+
+  - id: "comments"
+    type: "textarea"
+    attributes:
+      label: "Comments"
+      description: "Any additional comments you would like to add"

.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/[email protected]

.github/workflows/check-licenses.yml

@@ -13,6 +13,6 @@ jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: REUSE Compliance Check
-      uses: fsfe/reuse-action@v1
+      uses: fsfe/reuse-action@v5

.github/workflows/hermes-zenodo.yml

@@ -0,0 +1,151 @@
+# SPDX-FileCopyrightText: 2023 German Aerospace Center (DLR), Helmholtz-Zentrum Drseden-Rossendorf, Forschungszentrum Jülich
+#
+# SPDX-License-Identifier: CC0-1.0
+
+# SPDX-FileContributor: Stephan Druskat
+
+name: Software publication on Zenodo
+
+on:
+  push:
+    tags:
+      - "*"
+
+  # NOTE: Do not delete the trigger on closed pull requests, the HERMES workflow needs this.
+  pull_request:
+    types:
+      - closed
+
+jobs:
+  hermes-prepare:
+    name: Prepare Metadata for Curation
+    runs-on: ubuntu-latest
+    # This condition becomes much easier when we only react to push events on the release branch.
+    # We still need to exclude the merge commit push of the post processing PR
+
+    # ADAPT
+    # Depending on the event you react to in the 'on:' section above, you will need to adapt this
+    # to react on the specific events.
+    # NOTE: You will probably still need to keep the exclusion check for commit messages provided by the workflow ('hermes/'/'hermes/post').
+    if: >
+      github.event_name == 'push' && ! (
+        startsWith(github.ref_name, 'hermes/') ||
+        contains(github.event.head_commit.message, 'hermes/post')
+      )
+
+    permissions:
+      contents: write # Allow creation of new branches
+      pull-requests: write # Postprocessing should be able to create a pull request with changes
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+      - run: pip install hermes hermes-plugin-python
+      - run: hermes harvest
+      - run: hermes process
+      - run: hermes curate
+
+      - run: |
+          # Cache current branch for PR close job
+          git branch --show-current > .hermes/curate/target_branch
+
+          # Shorten the SHA for the PR title
+          SHORT_SHA=$(echo "$GITHUB_SHA" | cut -c -8)
+          echo "SHORT_SHA=$SHORT_SHA" >> "$GITHUB_ENV"
+
+          # Create a curation branch
+          git switch -c "hermes/curate-$SHORT_SHA"
+          git push origin "hermes/curate-$SHORT_SHA"
+
+          # Explicitly add to-be-curated metadata (which is ignored via .gitignore!)
+          git add -f .hermes/curate
+      - uses: peter-evans/create-pull-request@v7
+        with:
+          base: hermes/curate-${{ env.SHORT_SHA }}
+          branch: hermes/curate-result-${{ env.SHORT_SHA }}
+          title: Metadata Curation for Commit ${{ env.SHORT_SHA }}
+          body: |
+            Please carefully review the attached metadata.
+            If you are satisfied with the result, you may merge this PR, which will trigger publication.
+            (Any temporary branches will be cleaned up.)
+          delete-branch: true
+
+  hermes-curate:
+    name: Publish Software with Curated Metadata
+    if: github.event.pull_request.merged == true && startsWith( github.base_ref , 'hermes/curate-')
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write # Allow creation of new branches
+      pull-requests: write # Postprocessing should be able to create a pull request with changes
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+      - run: pip install hermes
+
+      # ADAPT
+      # If you want to publish artifacts (e.g., a zipped snapshot of your repository),
+      # you can prepare this here.
+      - run: git archive --format zip HEAD src > hermes.zip
+
+      # Run the HERMES deposition and postprocessing steps.
+      # ADAPT
+      # 1. You need to have an authentication token for your target publication platform
+      #    as a GitHub secret in your repository (in this example, this is called ZENODO_SANDBOX).
+      # 2. Adapt the files you want to deposit. In the example, showcase.zip and README.md are deposited alongside the metadata.
+      # 3. Check if you want to run with '--initial', as this may potentially create a completely new record (collection),
+      #    rather than a new version of the same collection!
+      - run: hermes deposit --initial -O invenio_rdm.auth_token ${{ secrets.ZENODO }} --file hermes.zip --file README.md
+
+      # ADAPT
+      # Remove this command if you don't want to do any postprocessing
+      - run: hermes postprocess
+
+      # ADAPT
+      # If you don't want to run postprocessing, remove this complete section (next '-run' and 'uses: peter-evans/...' bullets).
+      #
+      # Note 1: We change the base branch here for the PR. This flow runs so far within the "curated-metadata-*" branch,
+      #         but now we want to add the changes done by deposit and post processing to the branch that was initially
+      #         meant to be published using HERMES.
+      # Note 2: The create-pull-request action will NOT inherit the commits we did in the previous job. It will only look at the
+      #         changes within this local workspace we did *now*.
+      - run: echo "TARGET_BRANCH=$(cat .hermes/curate/target_branch)" >> "$GITHUB_ENV"
+      - uses: peter-evans/create-pull-request@v7
+        with:
+          branch: hermes/post-${{ github.run_id }}
+          base: ${{ env.TARGET_BRANCH }}
+          title: Review hermes post-processing results
+          body: |
+            This is an automated pull request created by HERMES post-processing.
+
+            Please carefully review the changes and finally merge them into your
+
+      # Delete all the curation branches
+      - run: |
+          for BRANCH in $(git ls-remote origin 'refs/heads/hermes/curate-*' | cut -f2 | cut -d'/' -f'3-'); do
+            git push origin --delete "$BRANCH"
+          done
+      # TODO: if: failure() --- delete the curation branches when the deposition failed
+
+
+  hermes-cleanup:
+    name: Cleanup aborted curation branches
+    if: github.event.pull_request.merged == false && startsWith( github.base_ref , 'hermes/curate-')
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write # Allow creation of new branches
+      pull-requests: write # Postprocessing should be able to create a pull request with changes
+
+    steps:
+      - uses: actions/checkout@v4
+      # Delete all the curation branches
+      - run: |
+          for BRANCH in $(git ls-remote origin 'refs/heads/hermes/curate-*' | cut -f2 | cut -d'/' -f'3-'); do
+            git push origin --delete "$BRANCH"
+          done

.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

.gitignore

@@ -23,3 +23,4 @@ dist/
 
 # HERMES workflow specifics
 .hermes/
+hermes.log

CITATION.cff

@@ -14,9 +14,9 @@ title: hermes
 message: >-
   If you use this software, please cite it using the
   metadata from this file.
-version: "0.8.0"
+version: 0.9.0
 license: "Apache-2.0"
-abstract: "Implementation of the HERMES workflow for FAIR software publication."
+abstract: "Tool to automate software publication. Not stable yet."
 type: software
 authors:
   - given-names: Michael
@@ -29,15 +29,10 @@ authors:
     email: [email protected]
     affiliation: German Aerospace Center (DLR)
     orcid: 'https://orcid.org/0000-0003-4925-7248'
-  - given-names: Jeffrey
-    family-names: Kelling
-    email: [email protected]
-    affiliation: Helmholtz-Zentrum Dresden-Rossendorf (HZDR)
-    orcid: 'https://orcid.org/0000-0003-1761-2591'
   - given-names: Oliver
     family-names: Bertuch
     email: [email protected]
-    affiliation: Forschungszentrum Jülich GmbH (FZJ)
+    affiliation: Forschungszentrum Jülich
     orcid: 'https://orcid.org/0000-0002-2702-3419'
   - given-names: Oliver
     family-names: Knodel
@@ -49,3 +44,17 @@ authors:
     email: [email protected]
     affiliation: Helmholtz-Zentrum Dresden-Rossendorf (HZDR)
     orcid: 'https://orcid.org/0000-0002-3145-9880'
+  - given-names: Kernchen
+    family-names: Sophie
+    email: [email protected]
+    affiliation: German Aerospace Center (DLR)
+    orcid: 'https://orcid.org/0009-0005-4430-6743'
+  - given-names: Nitai
+    family-names: Heeb
+    email: [email protected]
+    affiliation: Forschungszentrum Jülich
+    orcid: 'https://orcid.org/0009-0001-8382-4923'
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.13221384
+    description: Version 0.8.1b1