merge devel to master (#1382)

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,58 @@
+name: Bug report
+description: Create a bug report to help us eliminate issues and improve deepmd-kit.
+title: "[BUG] "
+labels: bug
+assignees: []
+body:
+  - type: textarea
+    id: summary
+    attributes:
+      label: Bug summary
+      description: Please provide a clear and concise description of what the bug is.
+      placeholder:
+      value:
+    validations:
+      required: true
+  - type: input
+    id: version
+    attributes:
+      label: DP-GEN Version
+      description: "`dpgen --version`"
+    validations:
+      required: true
+  - type: textarea
+    id: other-version
+    attributes:
+      label: Platform, Python Version, Remote Platform, etc
+      description: "If applicable, specify what platform you are running on."
+      placeholder:
+      value:
+    validations:
+      required: false
+  - type: textarea
+    id: log
+    attributes:
+      label: Input Files, Running Commands, Error Log, etc.
+      description: "Please provide necessary information including input file, running commands, error log , etc., AS  DETAILED AS POSSIBLE to help locate and reproduce your problem. WARNING: Do not use image to show error log! Paste texts in a code block instead."
+      placeholder:
+      value:
+    validations:
+      required: true
+  - type: textarea
+    id: reproduce
+    attributes:
+      label: Steps to Reproduce
+      description: "Describe the steps required to (quickly) reproduce the issue. You can attach (small) files to the section below or add URLs where to download an archive with all necessary files. Please try to create an input set that is as minimal and small as possible and reproduces the bug as quickly as possible. **NOTE:** the less effort and time it takes to reproduce your reported bug, the more likely it becomes, that somebody will look into it and fix the problem."
+      placeholder:
+      value:
+    validations:
+      required: true
+  - type: textarea
+    id: further
+    attributes:
+      label: Further Information, Files, and Links
+      description: Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications
+      placeholder:
+      value:
+    validations:
+      required: false

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,14 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Submit DeePMD-kit issue
+    url: https://github.com/deepmodeling/deepmd-kit/issues
+    about: If the issue is related to DeePMD-kit (model training and inference), submit to deepmd-kit repository
+  - name: Submit dpdata issue
+    url: https://github.com/deepmodeling/dpdata/issues
+    about: If the issue is related to dpdata (format conversion), submit to dpdata repository
+  - name: Submit dpdispatcher issue
+    url: https://github.com/deepmodeling/dpdispatcher/issues
+    about: If the issue is related to dpdispatcher (job submission), submit to dpdispatcher repository
+  - name: Request for Help
+    url: https://github.com/deepmodeling/dpgen/discussions/new?category=q-a
+    about: If you have an usage question

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,33 @@
+name: Feature request
+description: Suggest an idea for this project.
+title: "[Feature Request] "
+labels: enhancement
+assignees: []
+body:
+  - type: textarea
+    id: summary
+    attributes:
+      label: Summary
+      description: "Please provide a brief and concise description of the suggested feature or change"
+      placeholder:
+      value:
+    validations:
+      required: true
+  - type: textarea
+    id: details
+    attributes:
+      label: Detailed Description
+      description: "Please explain how you would like to see deepmd-kit enhanced, what feature(s) you are looking for, what specific problems this will solve. If possible, provide references to relevant background information like publications or web pages, and whether you are planning to implement the enhancement yourself or would like to participate in the implementation. If applicable add a reference to an existing bug report or issue that this will address."
+      placeholder:
+      value:
+    validations:
+      required: true
+  - type: textarea
+    id: further
+    attributes:
+      label: Further Information, Files, and Links
+      description: Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications
+      placeholder:
+      value:
+    validations:
+      required: false

.github/ISSUE_TEMPLATE/generic-issue.yml

@@ -0,0 +1,38 @@
+name: Generic issue
+description: For issues that do not fit any of the other categories.
+assignees: []
+body:
+  - type: textarea
+    id: summary
+    attributes:
+      label: Summary
+      description: "Please provide a clear and concise description of what the question is."
+      placeholder:
+      value:
+    validations:
+      required: true
+  - type: input
+    id: version
+    attributes:
+      label: DP-GEN Version
+      description: "`dpgen --version`"
+    validations:
+      required: true
+  - type: textarea
+    id: other-version
+    attributes:
+      label: Platform, Python Version, etc
+      description: "If applicable, specify what platform you are running on."
+      placeholder:
+      value:
+    validations:
+      required: false
+  - type: textarea
+    id: details
+    attributes:
+      label: Details
+      description: "Please explain the issue in detail here."
+      placeholder:
+      value:
+    validations:
+      required: true

.github/workflows/release.yml

@@ -33,6 +33,21 @@ jobs:
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   release-to-pypi:
-    uses: deepmodeling/workflows/.github/workflows/release-to-pypi.yml@main
-    secrets:
-      PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+    name: Release to pypi
+    runs-on: ubuntu-latest
+    permissions:
+        # IMPORTANT: this permission is mandatory for trusted publishing
+        id-token: write
+    steps:
+    - uses: actions/checkout@v3
+    - name: Setup python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.x
+        architecture: x64
+    - name: Install dependencies
+      run: python -m pip install build
+    - run: python -m build
+    - name: Publish a Python distribution to PyPI
+      if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/test.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8, 3.9]
+        python-version: ["3.9", "3.12"]
 
     steps:
     - uses: actions/checkout@v2
@@ -18,7 +18,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
-      run: pip install coverage git+https://github.com/materialsproject/pymatgen@b56698019098247ff54f50997a67c562b4375fc3 -e .
+      run: pip install -e .[test]
     - name: Test
       run: coverage run --source=./dpgen -m unittest -v && coverage report
     - uses: codecov/codecov-action@v3

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
     # there are many log files in tests
     # TODO: seperate py files and log files
@@ -12,22 +12,27 @@ repos:
         exclude: "^tests/.*$"
     -   id: check-yaml
         exclude: "^conda/.*$"
-    #-   id: check-json
+    -   id: check-json
+        exclude: "^examples/CH4-lebesgue/.*$"
     -   id: check-added-large-files
     -   id: check-merge-conflict
     -   id: check-symlinks
         exclude: "^tests/tools/run_report_test_output/.*$"
     -   id: check-toml
+    -   id: pretty-format-json
+        args:
+          - "--autofix"
+          - "--no-sort-keys"
+          - "--indent=4"
+        exclude: "^examples/CH4-lebesgue/.*$"
+
 # Python
--   repo: https://github.com/psf/black
-    rev: 22.12.0
-    hooks:
-    -   id: black-jupyter
--   repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.253
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.3
     hooks:
     - id: ruff
       args: ["--fix"]
+    - id: ruff-format
 # numpydoc
 -   repo: https://github.com/Carreau/velin
     rev: 0.0.12