Merge pull request #334 from naik-aakash/update-dependencies-workflow

Update dependencies & CI publish workflow

Author: naik-aakash

.github/release.yml

@@ -0,0 +1,23 @@
+changelog:
+  exclude:
+    authors: [ dependabot, github-actions ]
+    labels: [automated-pr]
+  categories:
+    - title: 🚀 New Features
+      labels:
+        - enhancement
+    - title: 🐛 Bug Fixes 
+      labels:
+        - bug
+    - title: Enhancements 🛠
+      labels:
+        - enhancement
+    - title: 📚 Documentation
+      labels:
+        - documentation
+    - title: 🧹 House-Keeping
+      labels:
+        - housekeeping
+    - title: 🔄 Other Changes
+      labels:
+        - "*"

.github/workflows/docker-publish.yml

@@ -3,7 +3,7 @@ name: Build and Push Docker Image
 on:
   workflow_dispatch:
   release:
-    types: [ created ] # Runs only when a new release is created
+    types: [ published ] # Runs only when a new release is published
 
 jobs:
   build-image:
@@ -36,10 +36,9 @@ jobs:
       run: |
         echo "IMAGE_NAME=`echo ${{github.repository}} | tr '[:upper:]' '[:lower:]'`" >>${GITHUB_ENV}
     
-    - name: Extract version from pyproject.toml
+    - name: Extract version from release tag
       run: |
-          VERSION=$(grep '^version = ' pyproject.toml | sed -E 's/version = "(.*)"/\1/')
-          echo "VERSION=$VERSION" >> $GITHUB_ENV
+        echo "VERSION=${{ github.event.release.tag_name }}" >> $GITHUB_ENV
 
     # Build Docker image with a custom Python version
     - name: Build Docker image (Python ${{ matrix.python-version }})
@@ -53,7 +52,7 @@ jobs:
         docker push ghcr.io/${{ env.IMAGE_NAME }}/autoplex-python-${{ matrix.python-version }}:${{ env.VERSION }}
 
   update-devcontainer:
-    if: github.event_name == 'release' && github.event.action == 'created'
+    if: github.event_name == 'release' && github.event.action == 'published'
     needs: build-image
     runs-on: ubuntu-latest
     steps:
@@ -89,5 +88,7 @@ jobs:
         title: Update devcontainer.json version tag
         body: Update devcontainer.json version tag to reflect release changes
         branch: update-devcontainer
+        labels: |
+            automated-pr
         delete-branch: true
         base: main

.github/workflows/docs.yml

@@ -5,7 +5,7 @@ on:
   push:
     branches: [ main ]
   release:
-    types: [ created ]
+    types: [ published ]
 
 # set GITHUB_TOKEN permissions to allow deployment to GitHub Pages
 permissions:

.github/workflows/python-package.yml

@@ -34,6 +34,9 @@ jobs:
         echo "VERSION=$TAG" >> $GITHUB_ENV
 
     - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0  # Fetch the entire Git history
+        
     - name: Run tests using Docker image for Python ${{ matrix.python-version }}
       run: |
         docker pull ghcr.io/autoatml/autoplex/autoplex-python-${{ matrix.python-version }}:${{ env.VERSION }}

.github/workflows/python-publish.yml

@@ -12,10 +12,48 @@ on:
     types: [published]
 
 jobs:
-  deploy:
+  update-changelog:
     runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+
+      - name: Fetch Version Tag & Release Notes
+        id: get_release_info
+        run: |
+          echo "VERSION=${{ github.event.release.tag_name }}" >> $GITHUB_ENV
+          echo "NOTES<<EOF" >> $GITHUB_ENV
+          gh release view ${{ github.event.release.tag_name }} --json body -q .body >> $GITHUB_ENV
+          echo "EOF" >> $GITHUB_ENV
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Insert Version Tag & Release Notes Below `# Changelog`
+        run: |
+          { echo "# Changelog"; echo; echo "## $VERSION"; echo; echo "$NOTES"; echo; tail -n +2 CHANGELOG.md; } > temp.md && mv temp.md CHANGELOG.md
+          
+      - name: Create Pull Request to push updated CHANGELOG.md
+        uses: peter-evans/create-pull-request@v7
+        with:
+          token: ${{ secrets.ACTION_SECRET }}
+          commit-message: update CHANGELOG
+          title: Update changelog with latest release notes
+          body: Update CHANGELOG.md to reflect release changes
+          branch: update-changelog
+          labels: |
+            automated-pr
+          delete-branch: true
+          base: main
 
+  deploy:
+    needs: update-changelog
+    runs-on: ubuntu-latest
     steps:
+    - name: Pause for 5 minutes to merge update Changelog PR
+      run: |
+          echo "Wait for 5 minutes to merge PR..."
+          sleep 300
+          echo "Resuming workflow..."
     - uses: actions/checkout@v4
     - name: Set up Python
       uses: actions/setup-python@v4
@@ -29,4 +67,4 @@ jobs:
       uses: pypa/[email protected]
       with:
         user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+        password: ${{ secrets.PYPI_API_TOKEN }}

pyproject.toml

@@ -1,6 +1,7 @@
 [build-system]
 requires = [
   "setuptools>=65.0.0",
+  "setuptools-scm>=8.0",
   "wheel",
 ]
 build-backend = "setuptools.build_meta"
@@ -12,7 +13,8 @@ readme = "README.md"
 keywords = ["high-throughput", "automated", "mlpotential"]
 license = { text = "GPL-3.0 license" }
 authors = [{ name = "Janine George", email = "[email protected]" }]
-version = "0.1.1"
+# version = "0.1.1"
+dynamic = ["version"]
 classifiers = [
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.10",
@@ -24,7 +26,7 @@ classifiers = [
 requires-python = ">=3.10,<3.12"
 dependencies = [
      "pymatgen>=2024.9.17.1",
-     "atomate2[strict]>=0.0.18",
+     "atomate2[strict]>=0.0.19",
      "ase==3.23.0",
      "matgl==1.1.3",
      "mace-torch==0.3.9",
@@ -62,9 +64,13 @@ docs = [
     "sphinxcontrib-mermaid",
 
 ]
+workflow-managers = [
+    "FireWorks==2.0.4",
+    "jobflow-remote==0.1.5"
+]
 strict = [
-     "pymatgen==2024.10.3", #?
-     "atomate2[strict]==0.0.18",
+     "pymatgen==2024.11.13", #?
+     "atomate2[strict]==0.0.19",
      "matgl==1.1.3",
      "quippy-ase==0.9.14; python_version < '3.12'",
      "torch==2.2.1",
@@ -81,10 +87,7 @@ strict = [
 dev = ["pre-commit>=2.12.1"]
 tests = ["pytest", "pytest-mock", "pytest-split", "pytest-cov", "types-setuptools"]
 
-[tool.versioningit.vcs]
-method = "git"
-default-tag = "0.0.1"
-
+[tool.setuptools_scm]
 
 [tool.cibuildwheel.linux]
 archs = ["auto64"]

tests/auto/phonons/test_jobs.py

@@ -133,7 +133,7 @@ def test_get_output(clean_dir, test_dir, memory_jobstore):
 
     responses = run_locally(job_here)
 
-    responses[job_here.uuid][1].output["rms"] == pytest.approx(0.1223)
+    assert responses[job_here.uuid][1].output["rms"] == pytest.approx(0.1223, abs=0.00001)
 
     input_dict = {"metrics": [[{"benchmark_phonon_rmse": 0.12230662063050536, "dft_imaginary_modes": True,
                                 "ml_imaginary_modes": False},
@@ -314,7 +314,7 @@ def test_dft_task_doc(
     mock_vasp(ref_paths, fake_run_vasp_kwargs)
 
     # run the flow or job and ensure that it finished running successfully
-    responses = run_locally(
+    _ = run_locally(
         dft_phonon_workflow,
         create_folders=True,
         ensure_success=True,
@@ -331,12 +331,9 @@ def test_dft_task_doc(
 def test_dft_phonopy_gen_data_manual_supercell_matrix(
         vasp_test_dir,
         mock_vasp,
-        test_dir,
         memory_jobstore,
         relax_maker,
         static_energy_maker,
-        ref_paths_check_sc_mat,
-        fake_run_vasp_kwargs,
         clean_dir
 ):
     path_to_struct = vasp_test_dir / "dft_ml_data_generation" / "POSCAR"
@@ -358,10 +355,29 @@ def test_dft_phonopy_gen_data_manual_supercell_matrix(
                                                supercell_settings=supercell_settings)
 
     # automatically use fake VASP and write POTCAR.spec during the test
-    mock_vasp(ref_paths_check_sc_mat, fake_run_vasp_kwargs)
+    ref_paths_manual_sc = {
+        "dft tight relax 1": "dft_ml_data_generation/manual_sc/tight_relax_1/",
+        "dft tight relax 2": "dft_ml_data_generation/manual_sc/tight_relax_2/",
+        "dft static": "dft_ml_data_generation/manual_sc/static/",
+        "dft phonon static 1/2": "dft_ml_data_generation/manual_sc/phonon_static_1/",
+        "dft phonon static 2/2": "dft_ml_data_generation/manual_sc/phonon_static_2/",
+    }
+
+    fake_run_vasp_manual_sc_kwargs = {
+        "dft tight relax 1": {"incar_settings": ["NSW", "ISMEAR"]},
+        "dft tight relax 2": {"incar_settings": ["NSW", "ISMEAR"]},
+        "dft static": {"incar_settings": ["NSW", "ISMEAR"],
+                       "check_inputs": ["incar", "poscar", "potcar"]},
+        "dft phonon static 1/2": {"incar_settings": ["NSW"],
+                                  "check_inputs": ["incar", "poscar", "potcar"]},
+        "dft phonon static 2/2": {"incar_settings": ["NSW"],
+                                  "check_inputs": ["incar", "poscar", "potcar"]},
+    }
+
+    mock_vasp(ref_paths_manual_sc, fake_run_vasp_manual_sc_kwargs)
 
     # run the flow or job and ensure that it finished running successfully
-    responses = run_locally(
+    _ = run_locally(
         dft_phonon_workflow,
         create_folders=True,
         ensure_success=True,
@@ -375,7 +391,6 @@ def test_dft_phonopy_gen_data_manual_supercell_matrix(
 def test_dft_random_gen_data_manual_supercell_matrix(
         vasp_test_dir,
         mock_vasp,
-        test_dir,
         memory_jobstore,
         relax_maker,
         ref_paths_check_sc_mat,
@@ -406,7 +421,7 @@ def test_dft_random_gen_data_manual_supercell_matrix(
     mock_vasp(ref_paths_check_sc_mat, fake_run_vasp_kwargs)
 
     # run the flow or job and ensure that it finished running successfully
-    responses = run_locally(
+    _ = run_locally(
         dft_rattled_workflow,
         create_folders=True,
         ensure_success=True,

tests/test_data/vasp/dft_ml_data_generation/manual_sc/phonon_static_1/inputs/INCAR

@@ -0,0 +1,26 @@
+ALGO = Normal
+EDIFF = 1e-07
+ENAUG = 1360
+ENCUT = 700.0
+GGA = Ps
+IBRION = -1
+ISIF = 3
+ISMEAR = 0
+ISPIN = 1
+ISYM = 0
+KSPACING = 0.2
+LAECHG = False
+LASPH = True
+LCHARG = False
+LELF = False
+LMIXTAU = True
+LOPTICS = False
+LREAL = False
+LVTOT = False
+LWAVE = False
+NELM = 200
+NPAR = 4
+NSW = 0
+PREC = Accurate
+SIGMA = 0.05
+SYMPREC = 1e-09

tests/test_data/vasp/dft_ml_data_generation/manual_sc/phonon_static_1/inputs/POSCAR

@@ -0,0 +1,16 @@
+Li4 Cl4
+1.0
+   5.0610971241896960   -0.0000006092523619   -0.0000003660074017
+  -0.0000006092815283    5.0610988165144262    0.0000007954914030
+  -0.0000003665234025    0.0000007959831166    5.0610955328987517
+Li Cl
+4 4
+direct
+   1.0019758471283773    0.0000000143884762    0.0000000107516982 Li
+   0.0000000034717687    0.4999999886037613    0.5000000122922756 Li
+   0.5000000719600592    0.0000000248133745    0.4999999239567003 Li
+   0.4999999835485269    0.4999999476935811    0.0000000407198897 Li
+   0.5000001417092435    0.0000000296706020    0.0000000704553358 Cl
+   0.4999999916177629    0.4999999860471361    0.4999998505436807 Cl
+   0.9999998367678485    0.9999999911917783    0.4999999574638707 Cl
+   0.9999999799704115    0.5000000175912831    0.0000001338165418 Cl

tests/test_data/vasp/dft_ml_data_generation/manual_sc/phonon_static_1/inputs/POTCAR.spec

@@ -0,0 +1,2 @@
+Li_sv
+Cl