Devel update

.git_archival.txt

@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

.gitattributes

@@ -0,0 +1 @@
+.git_archival.txt  export-subst

.github/workflows/release.yml

@@ -6,42 +6,16 @@ on:
       - 'v*'
 
 jobs:
-  conda-publish:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v2
-    - name: publish-to-conda
-      uses: felix5572/conda-publish-action@v1.9
-      with:
-        subdir: 'conda'
-        anacondatoken: ${{ secrets.ANACONDA_TOKEN }}
-        platforms: 'noarch'
-  construct-and-publish:
-    runs-on: ubuntu-latest
-    needs: conda-publish
-    steps:
-    - uses: actions/checkout@master
-    - uses: s-weigand/setup-conda@v1
-    - run: conda install constructor jinja2 -y
-    - run: constructor ./conda
-    - name: Upload to release
-      uses: softprops/action-gh-release@master
-      if: startsWith(github.ref, 'refs/tags/')
-      with:
-        files: dpgen-*.sh
-        repository: ${{ env.GITHUB_REPOSITORY }}
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   release-to-pypi:
     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
+    - uses: actions/checkout@v4
     - name: Setup python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.x
         architecture: x64

.github/workflows/test.yml

@@ -12,13 +12,14 @@ jobs:
         python-version: ["3.9", "3.12"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+    - run: pip install uv
     - name: Install dependencies
-      run: pip install -e .[test]
+      run: uv pip install --system -e .[test]
     - name: Test
       run: coverage run --source=./dpgen -m unittest -v && coverage report
     - uses: codecov/codecov-action@v4

.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: v4.5.0
+    rev: v4.6.0
     hooks:
     # there are many log files in tests
     # TODO: seperate py files and log files
@@ -28,7 +28,7 @@ repos:
 
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.4
+    rev: v0.4.1
     hooks:
     - id: ruff
       args: ["--fix"]

.readthedocs.yaml

@@ -10,15 +10,14 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.10"
-
+  jobs:
+    post_create_environment:
+      - pip install uv
+    post_install:
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install -r doc/requirements.txt
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
    configuration: doc/conf.py
 
 # If using Sphinx, optionally build your docs in additional formats such as PDF
 formats: all
-
-# Optionally declare the Python requirements required to build your docs
-python:
-   install:
-   - requirements: doc/requirements.txt

dpgen/generator/run.py

@@ -4437,20 +4437,18 @@ def post_fp_cp2k(iter_index, jdata, rfailed=None):
         sys_output = glob.glob(os.path.join(work_path, "task.%s.*/output" % ss))
         sys_output.sort()
         tcount += len(sys_output)
-        all_sys = None
+        all_sys = dpdata.MultiSystems(type_map=jdata["type_map"])
         for oo in sys_output:
-            _sys = dpdata.LabeledSystem(oo, fmt="cp2k/output")
-            # _sys.check_type_map(type_map = jdata['type_map'])
-            if all_sys is None:
-                all_sys = _sys
-            else:
-                all_sys.append(_sys)
+            _sys = dpdata.LabeledSystem(
+                oo, fmt="cp2kdata/e_f", type_map=jdata["type_map"]
+            )
+            all_sys.append(_sys)
+            icount += 1
 
-        icount += len(all_sys)
         if (all_sys is not None) and (len(all_sys) > 0):
             sys_data_path = os.path.join(work_path, "data.%s" % ss)
             all_sys.to_deepmd_raw(sys_data_path)
-            all_sys.to_deepmd_npy(sys_data_path, set_size=len(sys_output))
+            all_sys.to_deepmd_npy(sys_data_path)
 
     if tcount == 0:
         rfail = 0.0

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools>=61", "setuptools_scm[toml]>=6.2"]
+requires = ["setuptools>=61", "setuptools_scm[toml]>=7"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -19,7 +19,8 @@ classifiers = [
 ]
 dependencies = [
     'numpy>=1.14.3',
-    'dpdata>=0.2.16',
+    'dpdata>=0.2.17',
+    'cp2kdata>=0.6.6',
     'pymatgen>=2022.11.1',
     'ase',
     'monty>2.0.0',

tests/generator/test_post_fp.py

@@ -281,7 +281,7 @@ def setUp(self):
         post_fp(0, jdata)
         self.system_1 = dpdata.LabeledSystem("iter.000000/orig", fmt="deepmd/raw")
         self.system_2 = dpdata.LabeledSystem(
-            "iter.000000/02.fp/data.000", fmt="deepmd/raw"
+            "iter.000000/02.fp/data.000/C2H2N2", fmt="deepmd/raw"
         )