Merge pull request #186 from pyiron/main

Merge main

.ci_support/environment-docs.yml

@@ -1,11 +1,11 @@
 channels:
 - conda-forge
 dependencies:
-  - nbsphinx
-  - sphinx
-  - myst-parser
-  - numpy
-  - mpi4py
-  - pympipool
-  - ase
-  - scipy
+- nbsphinx
+- sphinx
+- myst-parser
+- numpy
+- mpi4py
+- pympipool
+- ase
+- scipy

.ci_support/environment-mpich.yml

@@ -1,11 +1,11 @@
 channels:
-  - conda-forge
+- conda-forge
 dependencies:
-  - coverage
-  - lammps =2023.08.02
-  - mpich
-  - numpy =1.26.0
-  - mpi4py =3.1.4
-  - pympipool =0.7.1
-  - ase =3.22.1
-  - scipy =1.11.3
+- coverage
+- lammps =2024.02.07
+- mpich
+- numpy =1.26.4
+- mpi4py =3.1.5
+- pympipool =0.7.17
+- ase =3.22.1
+- scipy =1.13.0

.ci_support/environment-old.yml

@@ -0,0 +1,10 @@
+channels:
+- conda-forge
+dependencies:
+- lammps =2022.06.23
+- openmpi
+- numpy =1.23.5
+- mpi4py =3.1.4
+- pympipool =0.7.0
+- ase =3.20.1
+- scipy =1.9.3

.ci_support/environment-openmpi.yml

@@ -1,11 +1,11 @@
 channels:
-  - conda-forge
+- conda-forge
 dependencies:
-  - coverage
-  - lammps =2023.08.02
-  - openmpi
-  - numpy =1.26.0
-  - mpi4py =3.1.4
-  - pympipool =0.7.1
-  - ase =3.22.1
-  - scipy =1.11.3
+- coverage
+- lammps =2024.02.07
+- openmpi
+- numpy =1.26.4
+- mpi4py =3.1.5
+- pympipool =0.7.17
+- ase =3.22.1
+- scipy =1.13.0

.ci_support/release.py

@@ -0,0 +1,61 @@
+def get_setup_version_and_pattern(setup_content):
+    depend_lst, version_lst = [], []
+    for l in setup_content:
+        if '==' in l:
+            lst = l.split('[')[-1].split(']')[0].replace(' ', '').replace('"', '').replace("'", '').split(',')
+            for dep in lst:
+                if dep != '\n':
+                    version_lst.append(dep.split('==')[1])
+                    depend_lst.append(dep.split('==')[0])
+
+    version_high_dict = {d: v for d, v in zip(depend_lst, version_lst)}
+    return version_high_dict
+
+
+def get_env_version(env_content):
+    read_flag = False
+    depend_lst, version_lst = [], []
+    for l in env_content:
+        if 'dependencies:' in l:
+            read_flag = True
+        elif read_flag:
+            lst = l.replace('-', '').replace(' ', '').replace('\n', '').split("=")
+            if len(lst) == 2:
+                depend_lst.append(lst[0])
+                version_lst.append(lst[1])
+    return {d:v for d, v in zip(depend_lst, version_lst)}
+
+
+def update_dependencies(setup_content, version_low_dict, version_high_dict):
+    version_combo_dict = {}
+    for dep, ver in version_high_dict.items():
+        if dep in version_low_dict.keys() and version_low_dict[dep] != ver:
+            version_combo_dict[dep] = dep + ">=" + version_low_dict[dep] + ",<=" + ver
+        else:
+            version_combo_dict[dep] = dep + "==" + ver
+
+    setup_content_new = ""
+    pattern_dict = {d:d + "==" + v for d, v in version_high_dict.items()}
+    for l in setup_content:
+        for k, v in pattern_dict.items():
+            if v in l:
+                l = l.replace(v, version_combo_dict[k])
+        setup_content_new +=l
+    return setup_content_new
+
+
+if __name__ == "__main__":
+    with open('pyproject.toml', "r") as f:
+        setup_content = f.readlines()
+
+    with open('environment.yml', "r") as f:
+        env_content = f.readlines()
+
+    setup_content_new = update_dependencies(
+        setup_content=setup_content[2:],
+        version_low_dict=get_env_version(env_content=env_content),
+        version_high_dict=get_setup_version_and_pattern(setup_content=setup_content[2:]),
+    )
+
+    with open('pyproject.toml', "w") as f:
+        f.writelines("".join(setup_content[:2]) + setup_content_new)

.github/dependabot.yml

@@ -3,6 +3,5 @@ updates:
 - package-ecosystem: pip
   directory: "/"
   schedule:
-    interval: weekly
-    day: monday
+    interval: "daily"
   open-pull-requests-limit: 10

.github/workflows/black.yml

@@ -1,5 +1,4 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+# This workflow is used to check the differences and find conflict markers or whitespace errors
 
 name: Black
 
@@ -13,8 +12,8 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - uses: psf/black@stable
       with:
         options: "--check --diff"
-        src: "./pylammpsmpi"
+        src: ./${{ github.event.repository.name }}

.github/workflows/coverage.yml

@@ -14,7 +14,7 @@ jobs:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - uses: conda-incubator/setup-miniconda@v2
       with:
         python-version: "3.11"
@@ -23,14 +23,11 @@ jobs:
         channel-priority: strict
         use-mamba: true
         environment-file: .ci_support/environment-openmpi.yml
-    - name: Setup
-      shell: bash -l {0}
-      run: |
-        pip install --no-deps .
     - name: Test
       shell: bash -l {0}
       run: |
-        coverage run --omit pylammpsmpi/_version.py -m unittest discover tests
-        coverage combine
+        pip install versioneer[toml]==0.29
+        pip install . --no-deps --no-build-isolation
+        coverage run  --omit="pylammpsmpi/_version.py,tests/*" -m unittest discover tests
     - name: Coveralls
       uses: coverallsapp/github-action@v2

.github/workflows/UpdateDependabotPR.yml → .github/workflows/dependabot.yml

@@ -1,4 +1,4 @@
-name: UpdateDependabotPR
+name: Update DependabotPR
 
 on:
   pull_request_target:
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     if: (github.actor == 'dependabot[bot]')
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           ref: ${{ github.event.pull_request.head.ref }} # Check out the head of the actual branch, not the PR
           fetch-depth: 0 # otherwise, you will fail to push refs to dest repo
@@ -24,6 +24,7 @@ jobs:
           to=$(echo "$PR_TITLE" | awk '{print $6}')
           sed -i "/${package}/s/${from}/${to}/g" .ci_support/environment-openmpi.yml
           sed -i "/${package}/s/${from}/${to}/g" .ci_support/environment-mpich.yml
+          sed -i "/${package}/s/${from}/${to}/g" binder/environment.yml
       - name: UpdateDependabotPR commit
         run: |
           git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"

.github/workflows/deploy.yml

@@ -1,32 +1,41 @@
+# This workflow is used to upload and deploy a new release to PyPi
+# Based on https://github.com/pypa/gh-action-pypi-publish
+
 name: PyPi Release
 
 on:
     push:
     pull_request:
+    workflow_dispatch:
 
-# based on https://github.com/pypa/gh-action-pypi-publish
 jobs:
   build:
+    if: startsWith(github.event.ref, 'refs/tags') || github.event_name == 'release'
     runs-on: ubuntu-latest
-
+    environment:
+      name: pypi
+      url: https://pypi.org/p/${{ github.event.repository.name }}
+    permissions:
+      id-token: write
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - uses: conda-incubator/setup-miniconda@v2.2.0
       with:
-        python-version: "3.11"
-
-    - name: Install dependencies
-      run: >-
-        python -m pip install --user --upgrade setuptools wheel
+        python-version: 3.11
+        mamba-version: "*"
+        channels: conda-forge
+        miniforge-variant: Mambaforge
+        channel-priority: strict
+        auto-update-conda: true
+        environment-file: .ci_support/environment-openmpi.yml
     - name: Convert dependencies
-      run: >-
-        sed -i 's/==/>=/g' setup.py; cat setup.py
+      run: |
+        cp .ci_support/environment-old.yml environment.yml
+        python .ci_support/release.py; cat pyproject.toml
     - name: Build
-      run: >-
+      shell: bash -l {0}
+      run: |
+        pip install versioneer[toml]==0.29
         python setup.py sdist bdist_wheel
     - name: Publish distribution 📦 to PyPI
-      if: startsWith(github.event.ref, 'refs/tags') || github.event_name == 'release'
-      uses: pypa/gh-action-pypi-publish@master
-      with:
-        user: __token__
-        password: ${{ secrets.pypi_password }}
+      uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/format_black.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         token: ${{ secrets.DEPENDABOT_WORKFLOW_TOKEN }}
         ref: ${{ github.event.pull_request.head.ref }} # Check out the head of the actual branch, not the PR

.github/workflows/pypicheck.yml

@@ -10,7 +10,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - uses: conda-incubator/setup-miniconda@v2
       with:
         python-version: "3.11"
@@ -22,5 +22,6 @@ jobs:
     - name: Setup
       shell: bash -l {0}
       run: |
-        pip install --no-deps .
+        pip install versioneer[toml]==0.29
+        pip install . --no-deps --no-build-isolation
         pip check

.github/workflows/unittests-mpich.yml

@@ -18,7 +18,7 @@ jobs:
         python-version: ['3.9', '3.10', '3.11', '3.12']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - uses: conda-incubator/setup-miniconda@v2
       with:
         python-version: ${{ matrix.python-version }}
@@ -27,11 +27,10 @@ jobs:
         channel-priority: strict
         use-mamba: true
         environment-file: .ci_support/environment-mpich.yml
-    - name: Setup
-      shell: bash -l {0}
-      run: |
-        pip install --no-deps .
     - name: Test
       shell: bash -l {0}
       timeout-minutes: 5
-      run: coverage run --omit pylammpsmpi/_version.py -m unittest discover tests
+      run: |
+        pip install versioneer[toml]==0.29
+        pip install . --no-deps --no-build-isolation
+        python -m unittest discover tests

.github/workflows/unittests-old.yml

@@ -0,0 +1,32 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Unittest Lower Bound
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        python-version: '3.9'
+        miniforge-variant: Mambaforge
+        channels: conda-forge
+        channel-priority: strict
+        use-mamba: true
+        environment-file: .ci_support/environment-old.yml
+    - name: Test
+      shell: bash -l {0}
+      timeout-minutes: 5
+      run: |
+        pip install versioneer[toml]==0.29
+        pip install . --no-deps --no-build-isolation
+        python -m unittest discover tests

.github/workflows/unittests-openmpi.yml

@@ -18,7 +18,7 @@ jobs:
         python-version: ['3.9', '3.10', '3.11', '3.12']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - uses: conda-incubator/setup-miniconda@v2
       with:
         python-version: ${{ matrix.python-version }}
@@ -27,11 +27,10 @@ jobs:
         channel-priority: strict
         use-mamba: true
         environment-file: .ci_support/environment-openmpi.yml
-    - name: Setup
-      shell: bash -l {0}
-      run: |
-        pip install --no-deps .
     - name: Test
       shell: bash -l {0}
       timeout-minutes: 5
-      run: coverage run --omit pylammpsmpi/_version.py -m unittest discover tests
+      run: |
+        pip install versioneer[toml]==0.29
+        pip install . --no-deps --no-build-isolation
+        python -m unittest discover tests