Merge pull request #115 from alchem0x2A/master

Update api update workflow and paper

Author: alchem0x2A

.github/workflows/publish-pypi.yml

@@ -19,10 +19,10 @@ jobs:
       id-token: write
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - uses: conda-incubator/setup-miniconda@v3
       with:
-        python-version: "3.10"
+        python-version: "3.11"
         mamba-version: "*"
         channels: conda-forge,defaults
         channel-priority: true

.github/workflows/update_api.yml

@@ -17,6 +17,9 @@ jobs:
       run:
         shell: bash -l {0}
     runs-on: ubuntu-latest
+    # Only the upstream repo runs the automatic API update
+    if: |
+      !github.event.repository.fork || github.event_name == 'workflow_dispatch'
 
     steps:
     - uses: actions/checkout@v4
@@ -48,37 +51,34 @@ jobs:
         echo UPDATE_NEEDED is "${UPDATE_NEEDED}"
         echo API version is "${API_VERSION}"
       continue-on-error: true
-    - name: Create PR body text
+    - name: Create or Update Pull Request
+      # Manually disable to make sure it can rerun
       if: env.UPDATE_NEEDED == 'true'
-      run: |
-        touch pr_body.txt
-        echo "## Automated JSON API Update" >> pr_body.txt
-        echo "Hello! This is an automatic pull request to merge the new JSON API version **${API_VERSION}** into the master branch." >> pr_body.txt
-        echo "### Details" >> pr_body.txt
-        echo "- **Workflow Trigger**: This update is triggered by the **Update JSON API (recurring job)** workflow." >> pr_body.txt
-        echo "- **Reason for Update**: A new JSON schema version was generated that differs from the existing one in the repository." >> pr_body.txt
-        echo "### Notes" >> pr_body.txt
-        echo "- If you notice any issues or have questions regarding this update, please contact @alchem0x2a or other maintainers of the repository." >> pr_body.txt
-        echo "Thank you for keeping the SPARC-X-API project up-to-date! 🚀" >> pr_body.txt
-        cat pr_body.txt
-    - name: Create Pull Request
-      # Do not create PR from another PR
-      if: (env.UPDATE_NEEDED == 'true') && (github.event_name != 'pull_request')
-      run: |
-        git config --global user.email "alchem0x2a@gmail.com"
-        git config --global user.name "Github Action Bot"
-        echo "New version is ${API_VERSION}"
-        BRANCH_NAME="update-api-${GITHUB_RUN_ID}"
-        echo "Checking new branch ${BRANCH_NAME}"
-        git checkout -b $BRANCH_NAME
-        mv parameters.json sparc/sparc_json_api/
-        git add sparc/sparc_json_api/parameters.json
-        git commit -m "Add new json api version ${API_VERSION}"
-        git push --force --set-upstream origin ${BRANCH_NAME}
+      uses: peter-evans/create-pull-request@v7
+      with:
+        token: ${{ secrets.GITHUB_TOKEN }}
+        commit-message: |
+          Update JSON API to version ${{ env.API_VERSION }}
+
+          The commit is created by a scheduled CI job.
+          ""
+        branch: update-api-${{ env.API_VERSION }}
+        title: "[Automated] Update JSON API to version ${{ env.API_VERSION }}"
+        body: |
+          ## Automated JSON API Update
+
+          Hello! This is an automatic pull request to merge the new JSON API to version **${{ env.API_VERSION }}**.
+
+          ### Details
+          - **Workflow Trigger:** Update JSON API (recurring job).
+          - **Reason for Update:** A new JSON schema version was generated that differs from the existing one in the repository.
+
+          ### Notes
+          - If you notice any issues or have questions regarding this update, please reach out to the maintainers.
 
-        gh pr create --base master \
-                     --title "[PR Bot] New JSON API version ${API_VERSION}"  \
-                     --body-file pr_body.txt \
-                     -R ${{ github.repository_owner }}/SPARC-X-API
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          # Eliminate unnecessary PRs if not closed
+          delete-branch: true
+          # Prevent PRs on forks
+          base: master
+        delete-branch: true
+        base: master

paper/paper.md

@@ -29,9 +29,9 @@ authors:
     corresponding: true
     affiliation: "1, 2"
 affiliations:
-  - name: College of Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
+  - name: College of Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States of America
     index: 1
-  - name: College of Computing, Georgia Institute of Technology, Atlanta, GA 30332, USA
+  - name: College of Computing, Georgia Institute of Technology, Atlanta, GA 30332, United States of America
     index: 2
   - name: Department of Chemical and Materials Engineering, University of Alberta, Edmonton AB, T6G 2R3, Canada
     index: 3

pyproject.toml

@@ -5,5 +5,5 @@
 #
 # Note: the actual installation is still handled by setup.py
 [build-system]
-requires = ["setuptools >= 64", "wheel"]
+requires = ["setuptools >= 64", "wheel", "setuptools-scm>=8"]
 build-backend = "setuptools.build_meta"

setup.py

@@ -5,6 +5,9 @@
 
 from setuptools import find_packages
 from setuptools.command.install import install
+from setuptools_scm import get_version
+
+print(f"Version from setuptools_scm is {get_version()}")
 
 test_requires = [
     "pytest",
@@ -25,7 +28,9 @@
 
 setup(
     name="sparc-x-api",
-    version="1.0.8",
+    # @TT 2025.06.07 we use setuptools_scm for future
+    # releases before fully transition to pyproject.toml
+    version=get_version(),
     python_requires=">=3.8",
     description="Python API for the SPARC DFT Code",
     long_description=open("README.md").read(),

sparc/common.py

@@ -1,6 +1,4 @@
-from pathlib import Path
+import importlib.resources
 
-import pkg_resources
-
-repo_dir = Path(pkg_resources.resource_filename("sparc", "."))
-psp_dir = Path(pkg_resources.resource_filename("sparc", "psp"))
+repo_dir = importlib.resources.files("sparc")
+psp_dir = repo_dir / "psp"

sparc/docparser.py

@@ -728,6 +728,7 @@ def sanitize_type(param_dict, suppress_warnings=False):
                     f"The error is {e}"
                 )
             _array_test = False  # Retain
+            _bool_test = False
 
         if _array_test is True:
             sanitized_type = f"{origin_type} array"
@@ -796,4 +797,4 @@ def sanitize_type(param_dict, suppress_warnings=False):
     with open(output, "w", encoding="utf8") as fd:
         fd.write(json_string)
     print(f"SPARC parameter specifications written to {output}!")
-    print("If you need to fintune the definitions, please edit them manually.")
+    print("If you need to finetune the definitions, please edit them manually.")