Bump versions (#38)

* Bump versions

* Update run_tests.yml

* Update light_python_wrapper

- Fix DuplicateSuperClass error
- Fix helpwin.xsl path change
- Add check for empty module in install_python_mod to return early

* Fix euphonic doc test for R2022b and newer

* Pin Brille to 0.7.0 as wheels for 0.8.0 crash on Windows

* Update readthedocs configurations

* Remove 1.3.1 version pin, revert to just latest Matlab in CI

* Update light_python_wrapper to latest main sha

* Switch to conda on Windows. Remove brille-0.7.0 pin

* Revert brille-0.7.0 pin as still segfaults on CI

---------

Co-authored-by: Duc Le <[email protected]>

+euphonic/install_python_modules.m

@@ -6,6 +6,9 @@ function install_python_modules()
     % >>  euphonic.install_python_modules
 
     req_mods = required_modules;
+    if isempty(req_mods)
+        return
+    end
 
     pipe = py.subprocess.PIPE;
     kwargs = pyargs('stdout', pipe, 'stderr', pipe);

.github/workflows/run_tests.yml

@@ -14,69 +14,62 @@ jobs:
       matrix:
         os: [windows-latest, ubuntu-latest]
         matlab_version: [latest]
-        python_version: [3.9]
+        python_version: [3.11]
         euphonic_version: ['']
         # Test lowest supported Python/Euphonic versions, and lowest available Matlab
         include:
           - os: ubuntu-latest
-            matlab_version: R2020a
-            python_version: 3.7
-            euphonic_version: '--version 1.2.0'
+            matlab_version: R2021b
+            python_version: 3.9
       fail-fast: false
     runs-on: ${{ matrix.os }}
     defaults:
       run:
         shell: bash -l {0}  # Needed to use conda environments
     steps:
       - name: Check out Horace-Euphonic-Interface
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: true
       - name: Set up MATLAB
-        uses: matlab-actions/setup-matlab@v1 # v1.1.0 required for Windows/MacOS support
+        uses: matlab-actions/setup-matlab@v2 # v1.1.0 required for Windows/MacOS support
         with:
           release: ${{ matrix.matlab_version }}
       - name: Set up Python
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           python-version: ${{ matrix.python_version }}
-      - name: Set Python environment variable for access by Matlab
-        if: ${{ matrix.os != 'windows-latest' }}
-        run: echo "PYTHON_EX_PATH=`which python`" >> $GITHUB_ENV
-      - name: Set Python environment variable for access by Matlab (Windows)
+          auto-update-conda: true
+          conda-solver: libmamba
+          channels: conda-forge
+      - name: Set up Python environment (Windows)
         if: ${{ matrix.os == 'windows-latest' }}
         shell: powershell
         run: |
+          python -m pip install requests psutil numpy==1.26.4 brille==0.7.0 euphonic[phonopy_reader]
           $pypath = (Get-Command python).Path
           echo "PYTHON_EX_PATH=$pypath" | Out-File -FilePath $Env:GITHUB_ENV -Encoding utf8 -Append
-      - name: Update pip and create Matlab toolbox
+      - name: Set up Python environment (Linux)
+        if: ${{ matrix.os == 'ubuntu-latest' }}
         run: |
-            python -m pip install --upgrade pip &&
-            python -m pip install requests &&
-            python create_mltbx.py
-      - name: Install base Euphonic
-        run: |
-            python -m pip install numpy &&
-            python euphonic_sqw_models/apply_requirements.py ${{ matrix.euphonic_version }}
-            python create_mltbx.py
+          python -m pip install requests psutil numpy==1.26.4 euphonic[phonopy_reader,brille]
+          echo "PYTHON_EX_PATH=`which python`" >> $GITHUB_ENV
+      - name: Create Matlab toolbox
+        run: python create_mltbx.py
+      - name: create_toolbox
+        uses: matlab-actions/run-command@v2
+        with:
+          command: cd('mltbx'); create_mltbx()
       - name: Run tests with base Euphonic
-        uses: matlab-actions/run-command@v1
+        uses: matlab-actions/run-command@v2
         with:
           command: cd('test'); set_up_dependencies; run_tests('not', 'phonopy_reader', 'not', 'brille')
-      - name: Install Euphonic phonopy_reader
-        if: always()
-        run: python euphonic_sqw_models/apply_requirements.py ${{ matrix.euphonic_version}} --extras phonopy_reader
       - name: Run tests with Euphonic and phonopy_reader
-        if: always()
-        uses: matlab-actions/run-command@v1
+        uses: matlab-actions/run-command@v2
         with:
           command: cd('test'); set_up_dependencies; run_tests('phonopy_reader')
-      - name: Install brille
-        if: always()
-        run: python euphonic_sqw_models/apply_requirements.py ${{ matrix.euphonic_version}} --extras brille
       - name: Run tests with Euphonic and Brille
-        if: always()
-        uses: matlab-actions/run-command@v1
+        uses: matlab-actions/run-command@v2
         with:
           command: cd('test'); set_up_dependencies; run_tests('brille')
       - uses: codecov/codecov-action@v3

.readthedocs.yaml

@@ -0,0 +1,35 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: doc/source/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#   - pdf
+#   - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - requirements: doc/requirements.txt

create_mltbx.py

@@ -1,58 +1,79 @@
-import os
+import fileinput
 import re
-import subprocess
 import shutil
-import glob
+import subprocess
+from pathlib import Path
 
-import versioneer
 import update_module_versions
+import versioneer
 
 __version__ = versioneer.get_version()
 
-HELPDOCSTR = '\n' \
-    '    % Overloaded help command to display Python help in Matlab\n' \
-    '    % To use it, please type\n' \
-    '    %\n' \
-    '    % >> import euphonic.help\n' \
-    '    % >> help <topic>\n' \
-    '    %\n' \
-    '    % where <topic> is a Python class or method which has been wrapped for use in Matlab.\n' \
-    '    % If the topic is not wrapped, the normal Matlab help is displayed.\n' \
-
-def replace_matlab_docstring(filename, replacement_str):
-    with open(filename) as f:
-        txt = f.read()
-    cm = [m.start() for m in re.finditer(r'\n\s*%', txt)]
-    nl = [m.start() for m in re.finditer(r'\n', txt)]
-    idx = [cm[idx] for idx in range(len(cm)) if cm[idx] == nl[idx]]
+HELPDOCSTR = """
+    % Overloaded help command to display Python help in Matlab
+    % To use it, please type
+    %
+    % >> import euphonic.help
+    % >> help <topic>
+    %
+    % where <topic> is a Python class or method which has been wrapped for use in Matlab.
+    % If the topic is not wrapped, the normal Matlab help is displayed.
+"""
+
+
+def replace_matlab_docstring(filename: Path, replacement_str: str):
+    txt = filename.read_text(encoding="utf-8")
+    comment = [m.start() for m in re.finditer(r'\n\s*%', txt)]
+    newline = [m.start() for m in re.finditer(r'\n', txt)]
+    idx = [cm for cm, nl in zip(comment, newline) if cm == nl]
     newtxt = txt[:idx[0]] + replacement_str + txt[idx[-1]:]
-    with open(filename, 'w') as f:
-        f.write(newtxt)
-
-def create_mltbx():
-    import fileinput
-    # replace version string
-    version = __version__.split('+')[0] if '+' in __version__ else __version__  # Matlab only accepts numbers
-    with fileinput.FileInput('mltbx/horace_euphonic_interface.prj', inplace=True) as prj:
+    filename.write_text(newtxt, encoding="utf-8")
+
+
+def create_mltbx(base_path: Path):
+    """
+    Create toolbox assuming files relative to `base_path`
+    """
+
+    # replace version string as MATLAB only accepts numbers
+    version = __version__.split('+')[0] if '+' in __version__ else __version__
+    base_path = base_path.absolute()
+
+    lpw_src = base_path / "light_python_wrapper"
+    eup_src = base_path / "+euphonic"
+    mdl_src = base_path / "euphonic_sqw_models" / "euphonic_sqw_models"
+    mltbx_path = base_path / 'mltbx'
+    lpw_dest = mltbx_path / "+light_python_wrapper"
+    eup_dest = mltbx_path / "+euphonic"
+    mdl_dest = mltbx_path / "euphonic_sqw_models" / "euphonic_sqw_models"
+
+    with fileinput.FileInput(mltbx_path / 'horace_euphonic_interface.prj', inplace=True) as prj:
         for line in prj:
-            # FileInput redirect stdout to the file, for inplace replacement; end='' means don't add extra newlines
-            print(line.replace('<param.version>1.0</param.version>', f'<param.version>{version}</param.version>'), end='')
+            # FileInput redirects stdout to the file, for inplace replacement
+            print(line.replace('<param.version>1.0</param.version>',
+                               f'<param.version>{version}</param.version>'), end='')
+
     update_module_versions.update_module_versions()
     # shutil.copytree expects destination to not exist
     for dest_folder in ['+light_python_wrapper', 'euphonic_sqw_models', '+euphonic']:
-        if os.path.isdir('mltbx/' + dest_folder): shutil.rmtree('mltbx/' + dest_folder)
-    shutil.copyfile('LICENSE', 'mltbx/LICENSE')
-    shutil.copyfile('CITATION.cff', 'mltbx/CITATION.cff')
-    shutil.copytree('light_python_wrapper/+light_python_wrapper', 'mltbx/+light_python_wrapper')
-    shutil.copytree('euphonic_sqw_models/euphonic_sqw_models', 'mltbx/euphonic_sqw_models/euphonic_sqw_models')
-    shutil.copytree('+euphonic', 'mltbx/+euphonic')
-    for fil in glob.glob('light_python_wrapper/helputils/*.m'): shutil.copy(fil, 'mltbx/+euphonic')
-    for fil in glob.glob('light_python_wrapper/helputils/private/*.m'): shutil.copy(fil, 'mltbx/+euphonic/private')
-    replace_matlab_docstring('mltbx/+euphonic/help.m', HELPDOCSTR)
-    replace_matlab_docstring('mltbx/+euphonic/doc.m', HELPDOCSTR.replace('help', 'doc'))
-    subprocess.run(['matlab', '-batch', 'create_mltbx'], cwd='mltbx')
-    print('.mltbx created')
+        if (dest := mltbx_path / dest_folder).is_dir():
+            shutil.rmtree(dest)
 
-if __name__ == '__main__':
-    create_mltbx()
+    for file in ('LICENSE', 'CITATION.cff'):
+        shutil.copy(file, mltbx_path)
 
+    shutil.copytree(lpw_src / "+light_python_wrapper", lpw_dest)
+    shutil.copytree(mdl_src, mdl_dest)
+    shutil.copytree(eup_src, eup_dest)
+    for fil in (lpw_src / "helputils").glob("*.m"):
+        shutil.copy(fil, eup_dest)
+    for fil in (lpw_src / "helputils/private").glob("*.m"):
+        shutil.copy(fil, eup_dest / "private")
+
+    replace_matlab_docstring(eup_dest / "help.m", HELPDOCSTR)
+    replace_matlab_docstring(eup_dest / "doc.m", HELPDOCSTR.replace('help', 'doc'))
+
+
+if __name__ == '__main__':
+    curr_path = Path(__file__).parent
+    create_mltbx(curr_path)

doc/requirements.txt

@@ -0,0 +1,2 @@
+sphinx==7.4.7
+sphinx_rtd_theme==2.0.0

doc/source/conf.py

@@ -14,6 +14,19 @@
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))
 
+# -- RTD setup ---------------------------------------------------------------
+# See: https://about.readthedocs.com/blog/2024/07/addons-by-default/
+import os
+
+# Define the canonical URL if you are using a custom domain on Read the Docs
+html_baseurl = os.environ.get("READTHEDOCS_CANONICAL_URL", "")
+
+# Tell Jinja2 templates the build is running on Read the Docs
+if os.environ.get("READTHEDOCS", "") == "True":
+    if "html_context" not in globals():
+        html_context = {}
+    html_context["READTHEDOCS"] = True
+
 
 # -- Project information -----------------------------------------------------
 

test/EuphonicHelpTest.m

@@ -57,11 +57,17 @@ function run_euphonic_doc_tests(testCase)
             import matlab.unittest.constraints.IsFalse
             txt_fc_noimport = eval_doc('doc euphonic.ForceConstants');
             txt_fc_import = eval_doc_import('doc euphonic.ForceConstants');
-            % Checks both cases called "web" with the "-helpbrowser" argument
-            testCase.verifySubstring(txt_fc_noimport{2}, 'helpbrowser');
-            testCase.verifySubstring(txt_fc_import{2}, 'helpbrowser');
-            % Checks the two text are different
-            testCase.verifyThat(strcmp(txt_fc_noimport{1}, txt_fc_import{1}), IsFalse);
+            if verLessThan('matlab', '9.13')
+                % Checks both cases called "web" with the "-helpbrowser" argument
+                testCase.verifySubstring(txt_fc_noimport{2}, 'helpbrowser');
+                testCase.verifySubstring(txt_fc_import{2}, 'helpbrowser');
+                % Checks the two text are different
+                testCase.verifyThat(strcmp(txt_fc_noimport{1}, txt_fc_import{1}), IsFalse);
+            else
+                % Doc system changed in R2020b does not use the "web" command any more.
+                testCase.verifySubstring(txt_fc_noimport{1}.Topic, 'ForceConstants');
+                testCase.verifySubstring(txt_fc_import{2}, 'helpbrowser');
+            end
             % Checks we still have hyperlinks in the imported version
             testCase.verifyThat(contains(txt_fc_import{1}, 'href'), IsTrue);
             % Checks that __init__ method is included

test/mymockfuncs/+matlab/+internal/+doc/+reference/getReferencePage.m

@@ -0,0 +1,9 @@
+function [docPage, displayText, primitive] = getReferencePage(varargin)
+    % Function to overload built-in "getReferencePage" function
+    global web_called_with;
+    web_called_with = varargin;
+    displayText = string.empty;
+    primitive = true;
+    docPage = [];
+end
+

test/set_up_dependencies.m

@@ -28,4 +28,4 @@
  % Set flags on Linux to avoid segfault with libraries
 if ~ispc
   py.sys.setdlopenflags(int32(10))
-end
+end

update_module_versions.py

@@ -4,11 +4,12 @@
 def get_module_versions():
     # gets the required module versions from `min_requirements.txt` file
     curdir = os.path.dirname(os.path.abspath(__file__))
-    req_file = os.path.join(
-        curdir, 'euphonic_sqw_models', 'min_requirements.txt')
-    if not os.path.isfile(req_file):
-        from update_dependencies import update_submodules
-        update_submodules('euphonic_sqw_models')
+    for submodule in [['light_python_wrapper', '+light_python_wrapper'],
+                      ['euphonic_sqw_models', 'min_requirements.txt']]:
+        if not os.path.isfile(os.path.join(curdir, *submodule)):
+            from update_dependencies import update_submodules
+            update_submodules(submodule[0])
+    req_file = os.path.join(curdir, 'euphonic_sqw_models', 'min_requirements.txt')
     with open(req_file, 'r') as minreq:
         reqstrs = minreq.read().splitlines()
     reqmods = []