Merge pull request #1242 from pyiron/pyproject

Switch from setup.py to pyproject.toml

.ci_support/environment-docs.yml

@@ -2,7 +2,7 @@ channels:
 - conda-forge
 dependencies:
 - nbsphinx
-- sphinx <6.1
+- sphinx
 - ase
 - defusedxml
 - future

.ci_support/environment.yml

@@ -23,4 +23,4 @@ dependencies:
 - seekpath =2.1.0
 - spglib =2.1.0
 - structuretoolkit =0.0.15
-- python-blosc2  # required by pytables
+- python-blosc2  # required by pytables

.ci_support/release.py

@@ -0,0 +1,79 @@
+import json
+
+
+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
+
+
+def convert_key(key, convert_dict):
+    if key not in convert_dict.keys():
+        return key
+    else:
+        return convert_dict[key]
+
+
+if __name__ == "__main__":
+    with open('.ci_support/pypi_vs_conda_names.json', 'r') as f:
+        name_conversion_dict = {v: k for k, v in json.load(f).items()}
+
+    with open('pyproject.toml', "r") as f:
+        setup_content = f.readlines()
+
+    with open('environment.yml', "r") as f:
+        env_content = f.readlines()
+
+    env_version_dict = {
+        convert_key(key=k, convert_dict=name_conversion_dict): v
+        for k, v in get_env_version(env_content=env_content).items()
+    }
+
+    setup_content_new = update_dependencies(
+        setup_content=setup_content[2:],
+        version_low_dict=env_version_dict,
+        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)

.ci_support/test_backwards.sh

@@ -7,7 +7,8 @@ for t in tests/backwards/*save.py; do
     python $t
 done
 
-pip install --no-deps .
+pip install versioneer[toml]==0.29
+pip install . --no-deps --no-build-isolation
 i=0;
 echo "Before loading";
 for t in tests/backwards/*load.py; do

.github/workflows/backwards.yml

@@ -14,10 +14,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Setup environment
+    - uses: actions/checkout@v4
+    - name: Merge environments
       run: |
-        python .ci_support/condamerge.py --base .ci_support/environment.yml --add .ci_support/environment-notebooks.yml > environment.yml
+        cp .ci_support/environment.yml environment.yml
+        tail --lines=+4 .ci_support/environment-notebooks.yml >> environment.yml
     - name: Setup Mambaforge
       uses: conda-incubator/setup-miniconda@v2
       with:
@@ -26,23 +27,10 @@ jobs:
         channels: conda-forge
         channel-priority: strict
         activate-environment: my-env
+        environment-file: environment.yml
         use-mamba: true
-    - name: Set cache date and number
-      run: |
-        echo "DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV
-        cat .github/variables/cache_number.env >> $GITHUB_ENV
-    - uses: actions/cache@v2
-      with:
-        path: /usr/share/miniconda3/envs/my-env
-        key: linux-64-py-3-10-conda-${{ hashFiles('environment.yml') }}-${{ env.DATE }}-${{ env.CACHE_NUMBER }}
-      id: cache
-    - name: Update environment
-      run: mamba env update -n my-env -f environment.yml
-      if: steps.cache.outputs.cache-hit != 'true'
-    - name: Setup
+    - name: Test
       shell: bash -l {0}
       run: |
         python .ci_support/pyironconfig.py
-    - name: Test
-      shell: bash -l {0}
-      run: ./.ci_support/test_backwards.sh
+        ./.ci_support/test_backwards.sh

.github/workflows/benchmarks.yml

@@ -10,30 +10,27 @@ on:
 
 jobs:
   benchmark:
-
     runs-on: ${{ matrix.operating-system }}
     strategy:
       matrix:
         include:
           - operating-system: macos-latest
-            python-version: '3.10'
-            label: osx-64-py-3-10
+            python-version: '3.11'
+            label: osx-64-py-3-11
             prefix: /Users/runner/miniconda3/envs/my-env
 
           - operating-system: windows-latest
-            python-version: '3.10'
-            label: win-64-py-3-10
+            python-version: '3.11'
+            label: win-64-py-3-11
             prefix: C:\Miniconda3\envs\my-env
 
           - operating-system: ubuntu-latest
-            python-version: '3.10'
-            label: linux-64-py-3-10
+            python-version: '3.11'
+            label: linux-64-py-3-11
             prefix: /usr/share/miniconda3/envs/my-env
 
     steps:
-      - uses: actions/checkout@v2
-      - name: Setup environment
-        run: cp .ci_support/environment.yml environment.yml
+      - uses: actions/checkout@v4
       - name: Setup Mambaforge
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -42,25 +39,13 @@ jobs:
           channels: conda-forge
           channel-priority: strict
           activate-environment: my-env
+          environment-file: .ci_support/environment.yml
           use-mamba: true
-      - name: Set cache date and number
-        run: |
-          echo "DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV
-          cat .github/variables/cache_number.env >> $GITHUB_ENV
-      - uses: actions/cache@v2
-        with:
-          path: ${{ matrix.prefix }}
-          key: ${{ matrix.label }}-conda-${{ hashFiles('environment.yml') }}-${{ env.DATE }}-${{ env.CACHE_NUMBER }}
-        id: cache
-      - name: Update environment
-        run: mamba env update -n my-env -f environment.yml
-        if: steps.cache.outputs.cache-hit != 'true'
-      - name: Setup
-        shell: bash -l {0}
-        run: |
-          python .ci_support/pyironconfig.py
-          pip install --no-deps .
       - name: Tests
         shell: bash -l {0}
         timeout-minutes: 30
-        run: python -m unittest discover test_benchmarks
+        run: |
+          python .ci_support/pyironconfig.py
+          pip install versioneer[toml]==0.29
+          pip install . --no-deps --no-build-isolation
+          python -m unittest discover test_benchmarks

.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: "./pyiron_atomistics"
+        src: ./${{ github.event.repository.name }}

.github/workflows/codeql-analysis.yml

@@ -13,7 +13,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         fetch-depth: 2
 

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

@@ -1,32 +1,33 @@
-name: UpdateDependabotPR
-
-on:
-  pull_request_target:
-    branches: [ main ]
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    if: (github.actor == 'dependabot[bot]')
-    steps:
-      - uses: actions/checkout@v2
-        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
-          token: ${{ secrets.DEPENDABOT_WORKFLOW_TOKEN }}
-      - name: UpdateEnvironmentFile
-        env:
-          PR_TITLE: ${{ github.event.pull_request.title }}
-        shell: bash -l {0}
-        run: |
-          python .ci_support/update_environment.py $PR_TITLE
-      - name: UpdateDependabotPR commit
-        run: |
-          git config --local user.email "[email protected]"
-          git config --local user.name "pyiron-runner"
-          git commit -m "[dependabot skip] Update environment" -a
-      - name: UpdateDependabotPR push
-        uses: ad-m/github-push-action@master
-        with:
-          github_token: ${{ secrets.DEPENDABOT_WORKFLOW_TOKEN }}
-          branch: ${{ github.event.pull_request.head.ref }}
+name: Update Dependabot
+
+on:
+  pull_request_target:
+    branches: [ main ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    if: (github.actor == 'dependabot[bot]')
+    steps:
+      - 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
+          token: ${{ secrets.DEPENDABOT_WORKFLOW_TOKEN }}
+      - name: UpdateEnvironmentFile
+        shell: bash -l {0}
+        run: |
+          package=$(echo "${{ github.event.pull_request.title }}" | awk '{print $2}')
+          from=$(echo "${{ github.event.pull_request.title }}" | awk '{print $4}')
+          to=$(echo "${{ github.event.pull_request.title }}" | awk '{print $6}')
+          sed -i "/${package}/s/${from}/${to}/g" .ci_support/environment.yml
+      - name: UpdateDependabotPR commit
+        run: |
+          git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git config --local user.name "github-actions[bot]"
+          git commit -m "[dependabot skip] Update environment" -a
+      - name: UpdateDependabotPR push
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.DEPENDABOT_WORKFLOW_TOKEN }}
+          branch: ${{ github.event.pull_request.head.ref }}