Merge branch 'libAtoms:main' into neb_attach

.github/workflows/docs.yml

@@ -103,12 +103,9 @@ jobs:
           cd docs
           make html
 
-# event type from https://stackoverflow.com/questions/61886993/in-github-actions-how-to-get-the-type-of-a-trigger-event-as-a-variable
-# conditional control ("if:") from https://docs.github.com/en/actions/using-jobs/using-conditions-to-control-job-execution
-# dependency from https://docs.github.com/en/actions/using-jobs/using-jobs-in-a-workflow
-
   deploy-docs:
-    if: github.event.action == 'push'
+    name: Publish documentation
+    if: startsWith(github.ref, "refs/tags/") 
     needs: build-docs
     runs-on: ubuntu-latest
 

.github/workflows/pytests.yml

@@ -41,12 +41,12 @@ jobs:
       - name: Install dependencies from pip
         run: |
           echo "numpy<2" >> $PIP_CONSTRAINT
-          python3 -m pip install wheel setuptools numpy scipy click matplotlib pyyaml spglib rdkit flake8 pytest pytest-cov requests
+          python3 -m pip install wheel setuptools numpy scipy click matplotlib pyyaml spglib rdkit==2024.3.3 flake8 pytest pytest-cov requests
 
       - name: Install latest ASE from pypi
         run: |
           echo PIP_CONSTRAINT $PIP_CONSTRAINT
-          python3 -m pip install ase 
+          python3 -m pip install ase
           echo -n "ASE VERSION "
           python3 -c "import ase; print(ase.__file__, ase.__version__)"
 
@@ -105,15 +105,27 @@ jobs:
         run: |
           echo "search for torch version"
           set +o pipefail
+
+          # echo "torch versions"
+          # python3 -m pip install torch==
+          # echo "torch versions to search"
+          # python3 -m pip install torch== 2>&1 | fgrep 'from versions' |
+          #                      sed -e 's/.*from versions: //' -e 's/)//' -e 's/,[ ]*/\n/g' | tac
+
           # search for available torch version with +cpu support
-          for torch_version_test in $( python3 -m pip install torch== 2>&1 | fgrep 'from versions' | 
-                                       sed -e 's/.*from versions: //' -e 's/)//' -e 's/,[ ]*/\n/g' | tac ); do
+          # for torch_version_test in $( python3 -m pip install torch== 2>&1 | fgrep 'from versions' |
+          #                              sed -e 's/.*from versions: //' -e 's/)//' -e 's/,[ ]*/\n/g' | tac ); do
+          wget https://pypi.org/pypi/torch/json -O torch_versions
+          for torch_version_test in $( python3 -c "import json; print(' '.join(json.load(open('torch_versions'))['releases'].keys()))" | sed 's/ /\n/g' | tac ); do
+              echo "check torch_version_test $torch_version_test"
               set +e
               python3 -m pip install --dry-run torch==${torch_version_test}+cpu \
-                                     -f https://download.pytorch.org/whl/torch_stable.html > /dev/null 2>&1
+                                     -f https://download.pytorch.org/whl/torch_stable.html 2>&1
               search_stat=$?
+              echo "got search_stat $search_stat"
               set -e
               if [ $search_stat == 0 ]; then
+                  echo "got valid +cpu version, exiting"
                   torch_version=${torch_version_test}
                   break
               fi
@@ -269,7 +281,7 @@ jobs:
           mpirun -n 2 pytest --cov=wfl --cov-report term --cov-config=tests/.coveragerc --cov-report term-missing --cov-report term:skip-covered --with-mpi -k mpi --cov-append
 
       - name: 'Upload Coverage Data'
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         if: env.coverage-on-version == matrix.python-version
         with:
           name: coverage-html-${{ matrix.python-version }}

README.md

@@ -10,38 +10,23 @@ For examples and more information see [documentation](https://libatoms.github.io
 
 `wfl` and its dependencies may be installed via `pip install wfl`. 
 
-NOTE: (as of 14 June 2024) `wfl` is only tested against the latest ASE pip release, currently v3.23.0. 
-For the time being, v3.22.1 is the minimum version listed as a (pip) prerequisite of `wfl`, because
-it at least mostly works, but it may not be fully compatible and is not actively tested.
 
 # Recent changes
 
-v0.2.3:
+v0.3.1:
 
-- Add wfl.generate.neb, with required improved support for passing ConfigSet.groups() to 
-  autoaparallelized functions
+- additional updates to file-based calculators for ASE v3.23.
+- fixes to parity plots
 
-- Improved handling of old and new style ase.calculators.espresso.Espresso initialization
+v0.3.0:
 
-v0.2.2:
+- Update the file-based calculators (Orca, FHI-Aims, Vasp, Quantum Espresso, Castep) to work 
+  with with ASE v3.23. This update breaks backwards-compatibility. For compatibility with with 
+  the ASE v3.22 see use wfl v0.2.8 or earlier. 
 
-- Improve checking of DFT calculator convergence
+v0.2.8:
 
-v0.2.1:
+- Latest version compatible with ASE v3.22.x. To install, use `pip install wfl==0.2.8`. 
 
-- Fix group iterator
+For older changes see [documentation](https://libatoms.github.io/workflow).
 
-v0.2.0:
-
-- Change all wfl operations to use explicit random number generator [pull 285](https://github.com/libAtoms/workflow/pull/285), to improve reproducibility of scripts and reduce the chances that on script rerun, cached jobs will not be recognized due to uncontrolled change in random seed (as in [issue 283](https://github.com/libAtoms/workflow/issues/283) and [issue 284](https://github.com/libAtoms/workflow/issues/284)).  Note that this change breaks backward compatibility because many functions now _require_ an `rng` argument, for example
-  ```python
-  rng = np.random.default_rng(1)
-  md_configs = md.md(..., rng=rng, ...)
-  ```
-
-v0.1.0:
-
-- make it possible to fire off several remote autoparallelized ops without waiting for their jobs to finish
-- multi-pass calculation in `Vasp`, to allow for things like GGA followed by HSE
-- MACE fitting, including remote jobs
-- various bug fixes

docs/source/conf.py

@@ -12,6 +12,8 @@
 #
 import os
 import sys
+from wfl import __version__
+
 sys.path.insert(0, os.path.abspath('../../wfl'))
 
 
@@ -21,6 +23,8 @@
 #copyright = '2021, N. Bernstein, T. K. Stenczel, E. Gelzinyte'
 author = 'N. Bernstein, T. K. Stenczel, E. Gelzinyte'
 
+release = __version__
+
 
 # -- General configuration ---------------------------------------------------
 

docs/source/index.rst

@@ -23,14 +23,6 @@ Quick start that installs all of the mandatory dependencies:
 
 	python3 -m pip install wfl
 
-.. note::
-
-    (as of 14 June 2024) `wfl` is only tested against the latest
-    ASE pip release, currently v3.23.0.  For the time being, v3.22.1 is
-    the mininum version listed as a (pip) prerequisite of `wfl`, because
-    it at least mostly works, but it may not be fully compatible and is
-    not actively tested.
-
 
 ***************************************
 Repository
@@ -39,6 +31,67 @@ Repository
 Please find the code, raise issues and cotribute at https://github.com/libAtoms/workflow.  
 
 
+***************************************
+Development
+***************************************
+
+To install all dependencies needed for running unit tests:
+
+.. code-block:: sh
+
+	python3 -m pip install /path/to/workflow[test] 
+
+
+Some of the `wfl` functions rely on the `quippy-ase` package, which currently (2 September 2024) supports no higher Python versions than v3.9.
+
+The file-based calculator tests need ASE calculator configiguration file to be present; `see the ASE documentation <https://wiki.fysik.dtu.dk/ase/ase/calculators/calculators.html#calculator-configuration>`. 
+
+
+***************************************
+Recent Changes
+***************************************
+
+v0.3.0:
+
+- Update the file-based calculators (Orca, FHI-Aims, Vasp, Quantum Espresso, Castep) to work 
+  with with ASE v3.23. This update breaks backwards-compatibility. For compatibility with with 
+  the ASE v3.22 see use wfl v0.2.7 or earlier. 
+
+v0.2.7:
+
+- Latest version compatible with ASE v3.22.x. To install, use `pip install wfl==0.2.7`. 
+
+v0.2.3:
+
+- Add wfl.generate.neb, with required improved support for passing ConfigSet.groups() to 
+  autoaparallelized functions
+
+- Improved handling of old and new style ase.calculators.espresso.Espresso initialization
+
+v0.2.2:
+
+- Improve checking of DFT calculator convergence
+
+v0.2.1:
+
+- Fix group iterator
+
+v0.2.0:
+
+- Change all wfl operations to use explicit random number generator [pull 285](https://github.com/libAtoms/workflow/pull/285), to improve reproducibility of scripts and reduce the chances that on script rerun, cached jobs will not be recognized due to uncontrolled change in random seed (as in [issue 283](https://github.com/libAtoms/workflow/issues/283) and [issue 284](https://github.com/libAtoms/workflow/issues/284)).  Note that this change breaks backward compatibility because many functions now _require_ an `rng` argument, for example
+  ```python
+  rng = np.random.default_rng(1)
+  md_configs = md.md(..., rng=rng, ...)
+  ```
+
+v0.1.0:
+
+- make it possible to fire off several remote autoparallelized ops without waiting for their jobs to finish
+- multi-pass calculation in `Vasp`, to allow for things like GGA followed by HSE
+- MACE fitting, including remote jobs
+- various bug fixes
+
+
 ***************************************
 Contents
 ***************************************

pyproject.toml

@@ -1,12 +1,12 @@
 [project]
 
 name = "wfl"
-version = "0.3.0"
 requires-python = ">=3.9"
 dependencies = [ "click>=7.0", "numpy<2", "ase>=3.22.1", "pyyaml", "spglib",
-                 "docstring_parser", "expyre-wfl", "universalSOAP" ]
+                 "docstring_parser", "expyre-wfl", "universalSOAP", "pandas" ]
 readme = "README.md"
 license = { file = "LICENSE" }
+dynamic = ["version"]
 
 [project.scripts]
     wfl = "wfl.cli.cli:cli"
@@ -16,3 +16,24 @@ license = { file = "LICENSE" }
 
 [tool.setuptools.packages.find]
     exclude = [ "test*" ]
+
+[tool.setuptools.dynamic]
+version = {attr  = "wfl.__version__"}
+
+[project.optional-dependencies]
+test = [
+    "pytest",
+    "mace-torch",
+    "quippy-ase",
+    "requests",
+    "rdkit==2024.3.3",
+]
+doc = [
+    "sphinx",
+    "sphinx_click",
+    "nbsphinx",
+    "myst_parser",
+    "sphinx_book_theme",
+]
+all = ["wfl[test,doc]"]
+