Merge pull request #135 from SCM-NV/DavidOrmrodMorley/sync-fix2024-20…

…24-08-20

Final manual sync from fix2024 in the amshome repo.

.flake8

@@ -1,3 +1,4 @@
 [flake8]
 exclude=doc, examples
+per-file-ignores = __init__.py:F401, setup.py:F821
 select=F

.github/workflows/ci.yml

@@ -0,0 +1,137 @@
+name: CI
+
+on:
+# Run on creating or updating a PR
+  pull_request:
+    types: [opened, synchronize, reopened]
+
+# And pushing to the trunk or fix branches
+  push:
+    branches:
+      - trunk
+      - 'fix*'
+
+# And pushing new version tags e.g. 2024.103
+    tags:
+      - '20[0-9]{2}\.[0-9]{3}'
+
+jobs:
+
+  unit-test:
+#   Run on ubuntu, mac and windows for python 3.8 (in AMS python stack) up to 3.11
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Move Repo To SCM Namespace and Set PYTHONPATH
+        if: runner.os != 'Windows'
+        run: |
+          mkdir -p scm/plams
+          find . -mindepth 1 -maxdepth 1 -not -name 'scm' -not -name '.*' -exec mv {} scm/plams/ \;
+          echo "PYTHONPATH=$(pwd):$PYTHONPATH" >> $GITHUB_ENV          
+
+      - name: Move Repo To SCM Namespace and Set PYTHONPATH (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          New-Item -Path scm\plams -ItemType Directory -Force
+          
+          Get-ChildItem -Directory | Where-Object { $_.Name -ne 'scm' } | ForEach-Object {
+            Move-Item -Path $_.FullName -Destination scm\plams
+          }
+
+          Get-ChildItem -File | ForEach-Object {
+            Move-Item -Path $_.FullName -Destination scm\plams
+          }
+
+          echo "PYTHONPATH=$(pwd);$env:PYTHONPATH" >> $env:GITHUB_ENV          
+
+      - name: Set Up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install Dependencies
+        working-directory: scm/plams
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install pytest
+          pip install coverage          
+
+      - name: Run Unit Tests
+        working-directory: scm/plams
+        run: |
+          pwd
+          coverage run -m pytest unit_tests
+#     ToDo: Bump the fail-under threshold over time until acceptable level is reached
+      - name: Evaluate Coverage
+        working-directory: scm/plams
+        run: coverage report --omit="unit_tests/*" -i --fail-under=25
+
+
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v4
+
+      - name: Set Up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
+      - name: Install Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install black
+          pip install "black[jupyter]"
+          pip install flake8          
+
+      - name: Run Black
+        run: |
+          black --check -t py38 -l 120 .          
+
+      - name: Run Flake8
+        run: |
+          flake8 --color never --count --config .flake8 .
+                    
+
+  build-docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v4
+
+      - name: Move Repo To SCM Namespace and Set PYTHONPATH
+        run: |
+          mkdir -p scm/plams
+          find . -mindepth 1 -maxdepth 1 -not -name 'scm' -not -name '.*' -exec mv {} scm/plams/ \;
+          echo "PYTHONPATH=$(pwd):$PYTHONPATH" >> $GITHUB_ENV          
+
+      - name: Set Up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
+      - name: Install Dependencies
+        working-directory: scm/plams
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          cd doc
+          pip install -r requirements.txt          
+
+#     Turn on the -W flag when building once warnings to external links have been resolved
+#     ToDo: add a warning allowlist to check the warnings logged via -w
+      - name: Build Sphinx Docs
+        working-directory: scm/plams/doc
+        run: |
+          python build_plams_doc          

doc/build_plams_doc

@@ -6,45 +6,48 @@ import sys
 from os.path import join as opj
 
 command = ""
-#Try to locate sphinx-build executable
-if 'AMSBIN' in os.environ:
-    command = opj(os.path.expandvars('$AMSBIN'), 'python3.5', 'bin', 'sphinx-build')
+# Try to locate sphinx-build executable
+if "AMSBIN" in os.environ:
+    command = opj(os.path.expandvars("$AMSBIN"), "python3.8", "bin", "sphinx-build")
     if not os.path.exists(command):
         # This might be a windows machine
-        command = opj(os.path.expandvars('$AMSBIN'), 'python3.5', 'Scripts', 'sphinx-build.exe')
+        command = opj(os.path.expandvars("$AMSBIN"), "python3.8", "Scripts", "sphinx-build.exe")
         if os.path.exists(command):
             # starting sphinx-build on windows is tricky...
-            command = ['sh', opj(os.path.expandvars('$AMSBIN'), 'amspython'), '-m', 'sphinx']
+            command = ["sh", opj(os.path.expandvars("$AMSBIN"), "amspython"), "-m", "sphinx"]
         else:
-            print('Warning: AMSBIN found in environment, but failed to locate sphinx-build')
+            print("Warning: AMSBIN found in environment, but failed to locate sphinx-build")
             command = ""
 if command == "":
-    null = open(os.devnull, 'wb')
+    null = open(os.devnull, "wb")
     try:
-        subprocess.call(['sphinx-build','--version'], stdout=null, stderr=null)
-        command = 'sphinx-build'
+        subprocess.call(["sphinx-build", "--version"], stdout=null, stderr=null)
+        command = "sphinx-build"
     except OSError:
         try:
-            subprocess.call(['sphinx-build2','--version'], stdout=null, stderr=null)
-            command = 'sphinx-build2'
+            subprocess.call(["sphinx-build2", "--version"], stdout=null, stderr=null)
+            command = "sphinx-build2"
         except OSError:
-            print('Error: Sphinx executable not found!')
+            print("Error: Sphinx executable not found!")
             null.close()
             sys.exit(0)
     null.close()
 
 location = os.path.dirname(os.path.realpath(__file__))
-#Source of documentation should be located in "source" subfolder next to this script
-source = opj(location, 'source')
+# Source of documentation should be located in "source" subfolder next to this script
+source = opj(location, "source")
 
-#Target can be given as command line argument, if not the "build" subfolder is used
+# Target can be given as command line argument, if not the "build" subfolder is used
 if len(sys.argv) > 1:
     target = sys.argv[1]
 else:
-    target = opj(location, 'build')
+    target = opj(location, "build")
 
+warning_file = "build_plams_doc_warn_errors.txt"
 if isinstance(command, list):
     # on windows command is a list of multiple items
-    subprocess.call(command + [source, target])
+    return_code = subprocess.call(command + [source, target, "-w", warning_file])
 else:
-    subprocess.call([command, source, target])
+    return_code = subprocess.call([command, source, target, "-w", warning_file])
+
+sys.exit(return_code)

doc/requirements.txt

@@ -0,0 +1,4 @@
+sphinx
+sphinx_copybutton
+sphinx_tabs
+ipython

doc/source/conf.py

@@ -21,7 +21,7 @@ def modify_signature(app, what, name, obj, options, signature, return_annotation
 
 def setup(app):
     if not tags.has("scm_theme"):
-        app.add_stylesheet("boxes.css")
+        app.add_css_file("boxes.css")
     app.add_directive("warning", Danger)
     app.add_directive("technical", Important)
     app.connect("autodoc-process-signature", modify_signature)
@@ -41,7 +41,7 @@ def setup(app):
 
 else:
 
-    extensions = []
+    extensions = ["sphinx_tabs.tabs"]
 
     # Add any paths that contain templates here, relative to this directory.
     templates_path = ["_templates"]

examples/QE_AMS_AFM_HubbardU.py

@@ -51,10 +51,7 @@ def get_settings() -> Settings:
         smearing="gaussian",
         degauss=0.02,
         nspin=2,
-        starting_magnetization=[
-            Settings(Label="Fe1", Value=1.0),
-            Settings(Label="Fe2", Value=-1.0)
-        ],
+        starting_magnetization=[Settings(Label="Fe1", Value=1.0), Settings(Label="Fe2", Value=-1.0)],
     )
 
     # You may also just use the normal PLAMS Settings dot notation

examples/ReactionEnergyBenchmark.py

@@ -110,12 +110,12 @@
 
 # summary.txt will contain a table similar to the below
 ##Method          HC7_1   HC7_2  HC7_3  HC7_4  HC7_5   HC7_6   HC7_7 ISOL6_1 ISOL6_2 ISOL6_3 ISOL6_4 ISOL6_5 (kcal/mol)
-#Truhlar_ref      14.34   25.02   1.90   9.81  14.84  193.99  127.22    9.77   21.76    6.82   33.52    5.30
-#Smith_wB97X_ref  28.77   41.09   1.75   6.26   9.30  238.83  157.65    9.32   20.80    1.03   26.43    0.40
-#ANI-1ccx         15.8    30.7   -0.2    7.7   11.7   196.5   127.9     9.2    21.5     3.8    35.4     6.9
-#ANI-2x           42.4    48.1   -1.9    5.4    8.0   238.4   156.9     7.9    20.8    -1.5    26.7     0.5
-#DFTB              7.1    19.0    0.2    3.6    5.4   223.5   150.8    11.7    22.6     7.9    35.2     8.6
-#ReaxFF           34.3    23.0   13.4    2.6    5.5   289.2   168.3    -9.2    24.2    70.7    30.9    89.3
-#ADF              20.8    31.4   -1.9    6.7    9.9   214.5   139.7     9.5    20.5     4.7    31.0     4.8
-#MP2              20.5    27.1    5.4    9.9   15.0   214.8   141.3    11.0    24.6     8.4    36.8     6.2
-#BAND             19.2    30.2   -2.7    7.3   11.0   218.5   141.3     9.9    18.5     5.3    31.7     4.7
+# Truhlar_ref      14.34   25.02   1.90   9.81  14.84  193.99  127.22    9.77   21.76    6.82   33.52    5.30
+# Smith_wB97X_ref  28.77   41.09   1.75   6.26   9.30  238.83  157.65    9.32   20.80    1.03   26.43    0.40
+# ANI-1ccx         15.8    30.7   -0.2    7.7   11.7   196.5   127.9     9.2    21.5     3.8    35.4     6.9
+# ANI-2x           42.4    48.1   -1.9    5.4    8.0   238.4   156.9     7.9    20.8    -1.5    26.7     0.5
+# DFTB              7.1    19.0    0.2    3.6    5.4   223.5   150.8    11.7    22.6     7.9    35.2     8.6
+# ReaxFF           34.3    23.0   13.4    2.6    5.5   289.2   168.3    -9.2    24.2    70.7    30.9    89.3
+# ADF              20.8    31.4   -1.9    6.7    9.9   214.5   139.7     9.5    20.5     4.7    31.0     4.8
+# MP2              20.5    27.1    5.4    9.9   15.0   214.8   141.3    11.0    24.6     8.4    36.8     6.2
+# BAND             19.2    30.2   -2.7    7.3   11.0   218.5   141.3     9.9    18.5     5.3    31.7     4.7

examples/ams_crs.py

@@ -35,7 +35,7 @@ def solubility():
     s.input.compound[0].frac1 = 1.0
 
     s.input.compound[1]._h = solute_coskf
-    s.input.compound[1].nring = 6 # number of ring atoms benzene
+    s.input.compound[1].nring = 6  # number of ring atoms benzene
     s.input.compound[1].meltingpoint = solute_properties["meltingpoint"]
     s.input.compound[1].hfusion = solute_properties["hfusion"] * Units.convert(
         1.0, "kJ/mol", "kcal/mol"

interfaces/adfsuite/ams.py

@@ -1230,9 +1230,7 @@ def tolist(x):
             else:
                 return [x]
 
-        conversion_ratio = Units.conversion_ratio("au", unit)
         sec = "History"
-        nEntries = self.readrkf(sec, "nEntries")
 
         items = [
             "IRCDirection",
@@ -1249,7 +1247,6 @@ def tolist(x):
         forw = {}
         back = {}
         reformed = {}
-        converged_mask = None
         forw_mask = None
         back_mask = None
         converged = self.get_history_property("Converged", history_section=sec)
@@ -1274,7 +1271,6 @@ def tolist(x):
                 back_mask = [x != 1 for x in d[k]]
                 d[k] = ["Forward" if x == 1 else "Backward" if x == 2 else x for x in d[k]]
 
-            n = len(d[k])
             forw[k] = list(compress(d[k], forw_mask))
             back[k] = list(compress(d[k], back_mask))
             back[k].reverse()
@@ -2275,10 +2271,10 @@ def get_runscript(self):
             ret += f'export SCM_SRUN_OPTIONS="$SCM_SRUN_OPTIONS -N {nnode}"\n'
         if _has_scm_pisa and isinstance(self.settings.input, DriverBlock):
             if self.settings.input.Engine.name == "QuantumESPRESSO":
-                ret += f"export SCM_DISABLE_MPI=1\n"
+                ret += "export SCM_DISABLE_MPI=1\n"
         else:
             if "QuantumEspresso" in self.settings.input:
-                ret += f"export SCM_DISABLE_MPI=1\n"
+                ret += "export SCM_DISABLE_MPI=1\n"
         if "preamble_lines" in self.settings.runscript:
             for line in self.settings.runscript.preamble_lines:
                 ret += f"{line}\n"
@@ -2509,7 +2505,7 @@ def _serialize_molecule(self):
 
         def serialize_to_settings(name, mol):
             if isinstance(mol, Molecule):
-                sett = serialize_molecule_to_settings(mol)
+                sett = serialize_molecule_to_settings(mol, name)
             elif _has_scm_unichemsys and isinstance(mol, ChemicalSystem):
                 sett = serialize_unichemsys_to_settings(mol)
 
@@ -2524,7 +2520,7 @@ def serialize_unichemsys_to_settings(mol):
             sett = InputParserFacade().to_settings(AMSJob._command, str(mol))
             return sett.ams.system[0]
 
-        def serialize_molecule_to_settings(mol):
+        def serialize_molecule_to_settings(mol, name: str = None):
             sett = Settings()
 
             if len(mol.lattice) in [1, 2] and mol.align_lattice():

interfaces/adfsuite/crs.py

@@ -108,7 +108,7 @@ def get_results(self, section=None) -> dict:
             raise ValueError("Results object is missing or incomplete.")
 
         # first get the two ranges for the indices
-        ncomp  = self.readkf(section, "ncomp")
+        ncomp = self.readkf(section, "ncomp")
         nitems = self.readkf(section, "nitems")
         try:
             nstruct = self.readkf(section, "nstruct")
@@ -142,17 +142,17 @@ def get_multispecies_dist(self):
         This function returns multispecies distribution for each (compound,structure) pair.  The format is a list
         with indices corresponding to compound indices.  Each item in the list is a dictionary with a structure name : list pair, where the structure name corresponds to a structure the compound can be exist as and the list is the distribution of that compound in that structure over the number of points (mole fractions, temperatures, pressures).
         """
-        res           = self.get_results()
+        res = self.get_results()
         property_name = res["property"].rstrip()
 
-        if(property_name=="LOGP"): 
+        if property_name == "LOGP":
             nPhase = 2
         else:
             nPhase = 1
 
-        ncomp         = self.readkf(self.section, "ncomp")
-        struct_names  = res["struct names"]
-        num_points    = self.readkf(self.section, "nitems")
+        ncomp = self.readkf(self.section, "ncomp")
+        struct_names = res["struct names"]
+        num_points = self.readkf(self.section, "nitems")
         valid_structs = [[] for _ in range(ncomp)]
         comp_dist = res["comp distribution"].flatten()
         for i in range(len(struct_names)):

mol/molecule.py

@@ -5,7 +5,6 @@
 import math
 import os
 from collections import OrderedDict
-from typing import List
 
 import numpy as np
 
@@ -23,7 +22,7 @@
 from scm.plams.tools.units import Units
 
 input_parser_available = "AMSBIN" in os.environ
-from typing import Dict, List, Optional, Tuple, Union, overload
+from typing import List, Optional, Tuple, overload
 
 __all__ = ["Molecule"]
 
@@ -2343,7 +2342,6 @@ def get_translated_vectors(iat, neighbors, molcoords):
             return
 
         # Get the lattice vectors, and make sure there are 3 of them
-        nats = len(self)
         latticevecs = []
         for i in range(3):
             if i < len(self.lattice):