Merge branch 'main' into ase_version_qe

.github/workflows/docs.yml

@@ -79,14 +79,12 @@ jobs:
 
             git clone https://github.com/phonopy/phonopy
             cd phonopy
-            python3 setup.py build
-            python3 -m pip install .
+            python3 -m pip install -e .
             cd ..
 
             git clone https://github.com/phonopy/phono3py
             cd phono3py
-            python3 setup.py build
-            python3 setup.py install
+            python3 -m pip install -e .
             cd ..
 
       - name: Install Quippy from PyPI

.github/workflows/pytests.yml

@@ -19,6 +19,7 @@ jobs:
     env:
       coverage-on-version: "3.9"
       use-mpi: True
+      PIP_CONSTRAINT: pip_constraint.txt
     defaults:
       run:
         shell: bash -l {0}
@@ -38,10 +39,13 @@ jobs:
           python3 --version
 
       - name: Install dependencies from pip
-        run: python3 -m pip install wheel setuptools numpy scipy click matplotlib pyyaml spglib rdkit flake8 pytest pytest-cov requests
+        run: |
+          echo "numpy<2" >> $PIP_CONSTRAINT
+          python3 -m pip install wheel setuptools numpy scipy click matplotlib pyyaml spglib rdkit flake8 pytest pytest-cov requests
 
-      - name: Install latest ASE from gitlab
+      - name: Install latest ASE from pypi
         run: |
+          echo PIP_CONSTRAINT $PIP_CONSTRAINT
           python3 -m pip install ase 
           echo -n "ASE VERSION "
           python3 -c "import ase; print(ase.__file__, ase.__version__)"
@@ -62,27 +66,28 @@ jobs:
         run: |
             # find mklvars
             for pkg in $( apt list --installed | fgrep "installed" | fgrep "mkl" | sed "s#/.*##" ); do
-                if dpkg -L $pkg | egrep -q 'vars.sh$'; then
-                    mklvars=$( dpkg -L $pkg | egrep 'vars.sh$' )
+                if dpkg -L $pkg | egrep -q 'env/vars.sh$'; then
+                    mklvars=$( dpkg -L $pkg | egrep 'env/vars.sh$' )
                     break
                 fi
             done
-            if [ -z $mklvars ]; then
-                echo 'Failed to find *vars.sh in any pkg named *mkl*'
+            if [ $( echo $mklvars | wc -w ) != 1 ]; then
+                echo "wrong number of  mkl setvars.sh '$mklvars'" 1>&2
                 exit 1
             fi
             source $mklvars intel64
 
+            export PIP_CONSTRAINT=$PWD/$PIP_CONSTRAINT
+
             git clone https://github.com/phonopy/phonopy
             cd phonopy
-            python3 setup.py build
-            python3 -m pip install .
+            echo python3 -m pip install -e . -vvv
+            python3 -m pip install -e . -vvv
             cd ..
 
             git clone https://github.com/phonopy/phono3py
             cd phono3py
-            python3 setup.py build
-            python3 setup.py install
+            python3 -m pip install -e . -vvv
             cd ..
 
       - name: Install Quippy from PyPI
@@ -99,16 +104,32 @@ jobs:
         run: |
           echo "search for torch version"
           set +o pipefail
-          torch_version=$( python3 -m pip install torch== 2>&1 | fgrep 'from versions' | sed -e 's/.* //' -e 's/)//' )
-          echo "found torch version $torch_version, installing cpu-only variant"
+          # search for available torch version with +cpu support
+          for torch_version_test in $( python3 -m pip install torch== 2>&1 | fgrep 'from versions' | 
+                                       sed -e 's/.*from versions: //' -e 's/)//' -e 's/,[ ]*/\n/g' | tac ); do
+              set +e
+              python3 -m pip install --dry-run torch==${torch_version_test}+cpu \
+                                     -f https://download.pytorch.org/whl/torch_stable.html > /dev/null 2>&1
+              search_stat=$?
+              set -e
+              if [ $search_stat == 0 ]; then
+                  torch_version=${torch_version_test}
+                  break
+              fi
+          done
+          if [ -z $torch_version ]; then
+              echo "Failed to find any pytorch version with +cpu variant" 1>&2
+              exit 1
+          fi
+          echo "found torch version ${torch_version}+cpu, installing"
           python3 -m pip install torch==${torch_version}+cpu -f https://download.pytorch.org/whl/torch_stable.html
           echo "installing mace"
           python3 -m pip install git+https://github.com/ACEsuit/mace.git@main
           python3 -c "import mace; print(mace.__file__)"
 
       - name: Julia and ace fit
         run: |
-          python3 -m pip install pip install threadpoolctl
+          python3 -m pip install threadpoolctl
           wget https://julialang-s3.julialang.org/bin/linux/x64/1.8/julia-1.8.1-linux-x86_64.tar.gz
           tar xzf julia-1.8.1-linux-x86_64.tar.gz
           # note that this hardwires a particular compatible ACE1pack version
@@ -215,10 +236,6 @@ jobs:
       - name: Test with pytest - coverage
         if: env.coverage-on-version == matrix.python-version
         run: |
-          echo "BOB pre actual pytest"
-          which python3
-          python3 -m pip list | grep numpy
-          python3 -c "import numpy; print(numpy.__file__, numpy.__version__)"
           rm -rf $HOME/pytest_cov
           mkdir $HOME/pytest_cov
           #

README.md

@@ -8,10 +8,10 @@ The main functions of Workflow is to efficiently parallelise operations over a s
 
 For examples and more information see [documentation](https://libatoms.github.io/workflow/)
 
-`wfl` and its dependendensies may be installed via `pip install wfl`. 
+`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 mininum version listed as a (pip) prerequisite of `wfl`, because
+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
@@ -41,7 +41,7 @@ v0.2.0:
 
 v0.1.0:
 
-- make it possible to fire off several remote autoparallellized ops without waiting for their jobs to finish
-- multi-pass calclation in `Vasp`, to allow for things like GGA followed by HSE
+- 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/examples.daisy_chain_mlip_fitting.ipynb

@@ -620,14 +620,13 @@
     "\n",
     "ref_errors = {\n",
     "    'atomization_energy/atom': {\n",
-    "        'train': {'RMSE': 0.026086070005729697, 'MAE': 0.02188233965637977, 'count': 50},\n",
-    "        '_ALL_': {'RMSE': 0.02631013293566519, 'MAE': 0.02217457525203221, 'count': 100},\n",
-    "        'test': {'RMSE': 0.026532303741682858, 'MAE': 0.02246681084768465, 'count': 50}},\n",
+    "        'train': {'RMSE': 0.020425437431681327, 'MAE': 0.016212666323964592, 'count': 50}, \n",
+    "        '_ALL_': {'RMSE': 0.01965484792256244, 'MAE': 0.015378010911287552, 'count': 100}, \n",
+    "        'test': {'RMSE': 0.01885278757750655, 'MAE': 0.014543355498610513, 'count': 50}}, \n",
     "    'forces/comp': {\n",
-    "        'train': {'RMSE': 0.6700484048236104, 'MAE': 0.48912067870708253, 'count': 5097},\n",
-    "        '_ALL_': {'RMSE': 0.674843619212047, 'MAE': 0.49305958821652923, 'count': 10188},\n",
-    "        'test': {'RMSE': 0.6796105918104188, 'MAE': 0.49700313992928696, 'count': 5091}}\n",
-    "}\n",
+    "        'train': {'RMSE': 0.6318812940305143, 'MAE': 0.4633571169452562, 'count': 5133},\n",
+    "        '_ALL_': {'RMSE': 0.6455044814693653, 'MAE': 0.4741960245074422, 'count': 10212}, \n",
+    "        'test': {'RMSE': 0.6589864341996843, 'MAE': 0.48515017148848205, 'count': 5079}}}\n",
     "\n",
     "print(errors)\n",
     "\n",

pyproject.toml

@@ -3,7 +3,7 @@
 name = "wfl"
 version = "0.3.0"
 requires-python = ">=3.9"
-dependencies = [ "click>=7.0", "numpy", "ase>=3.22.1", "pyyaml", "spglib",
+dependencies = [ "click>=7.0", "numpy<2", "ase>=3.22.1", "pyyaml", "spglib",
                  "docstring_parser", "expyre-wfl", "universalSOAP" ]
 readme = "README.md"
 license = { file = "LICENSE" }