Merge pull request #234 from alchem0x2A/master

.conda/README.md

@@ -1,4 +1,9 @@
 # Build conda recipe for sparc
+
+**Note** the official conda-forge package for SPARC can be found at
+[`sparc-x`](https://github.com/conda-forge/sparc-x-feedstock). This
+recipe is maintained for CI purpose only.
+
 1. Install `conda-build` and (optionally) `boa`
 ```bash
 conda install -c conda-forge "conda-build>=3.20" colorama pip ruamel ruamel.yaml rich mamba jsonschema
@@ -22,16 +27,9 @@ anaconda login
 anaconda upload $CONDA_PREFIX/conda-bld/linux-64/sparc-<YYYY>.<MM>.<DD>-<i>.bz2
 ```
 
-If the SPARC package is finally in production, we need to merge it to `conda-forge` channel (perhaps using a different name `sparc-dft`?)
-
 
 4. Using the package
 ```bash
 conda install -c <your-channel> sparc
 ```
 This will automatically install `sparc` with `openmpi` + `scalapack` + `openblas` support. No compilation requires afterwards.
-
-5. TODOs
-- [ ] Configure the mpi-aware fftw package
-- [ ] Include mkl-variant?
-- [ ] Complete conda-forge merge once in upstream main 

.github/workflows/build-test.yml

@@ -10,13 +10,41 @@ on:
   workflow_dispatch:
 
 jobs:
+  # Check if initialization.c is up-to-date with Changelog
+  package-date-check:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/checkout@v4
+    - uses: conda-incubator/setup-miniconda@v3
+      with:
+        python-version: "3.11"
+        activate-environment: sparc-test
+        conda-build-version: "24.9.0"
+        miniforge-version: latest # Fix according to https://github.com/conda-incubator/setup-miniconda?tab=readme-ov-file#example-10-miniforge
+        channels: conda-forge,defaults
+        channel-priority: true
+    - name: Install SPARC-X-API stable version for docparser
+      run: |
+        mamba install -c conda-forge pip setuptools
+        pip install git+https://github.com/SPARC-X/[email protected]
+    - name: Convert parameters.json
+      run: |
+        python -m sparc.docparser --include-subdirs doc/.LaTeX
+    - name: Check package version and ChangeLog date
+      run: |
+        # Usage:
+        # python test-outdated-package.py <parameters.json> <changelog>
+        python .github/workflows/test-outdated-package.py \
+               ./parameters.json ChangeLog
   build-linux:
     runs-on: ubuntu-latest
     defaults:
       run:
         shell: bash -l {0}
-    strategy:
-      max-parallel: 5
+    needs: package-date-check
 
     steps:
     - uses: actions/checkout@v4

.github/workflows/test-missing-parameters.py

@@ -0,0 +1,87 @@
+"""Test script to check parameters coverage in examples
+"""
+import json
+import os
+from pathlib import Path
+from sparc.io import _read_inpt
+
+def load_parameters_json(json_path):
+    """
+    Load the parameters from the parameters.json file.
+    """
+    with open(json_path, 'r') as f:
+        parameters = json.load(f)
+    if "parameters" not in parameters:
+        raise KeyError("The 'parameters' field is missing in parameters.json")
+    return parameters["parameters"]
+
+def check_missing_parameters(test_dir, parameters_json_path):
+    """
+    Check for missing parameters in the documentation.
+    test_dir must be structured in <name>/standard/<name>.inpt
+    """
+    test_dir = Path(test_dir)
+    documented_parameters = load_parameters_json(parameters_json_path)
+
+    # Iterate through the .inpt files and check for missing parameters
+    report = {}
+    for match_file in test_dir.glob("*/standard/*.inpt"):
+        test_name = match_file.stem
+        try:
+            inpt_data = _read_inpt(match_file)
+            params_in_file = inpt_data["inpt"]["params"]
+        except Exception:
+            # Something could be buggy with SPARC-X-API?
+            pass
+
+        # Check missing or typo parameters
+        missing_params = [
+            param for param in params_in_file
+            if (param.upper() not in documented_parameters)
+            # TODO: Obsolete BOUNDARY_CONDITION keyword
+            and (param.upper() != "BOUNDARY_CONDITION")
+        ]
+        if missing_params:
+            report[test_name] = missing_params
+
+    # Generate report and return error if missing parameters are found
+    if report:
+        print("Missing / Incorrect Parameters Report:")
+        print("-" * 60)
+        for file_path, missing_params in report.items():
+            print(f"Test name: {file_path}")
+            print(f"Missing Parameters: {', '.join(missing_params)}")
+            print("-" * 60)
+        return False
+    else:
+        print("All parameters are documented correctly.")
+        return True
+
+
+def main():
+    import argparse
+    parser = argparse.ArgumentParser(
+        description="Check for missing / incorrect parameters in SPARC examples."
+    )
+    parser.add_argument(
+        "test_directory",
+        type=str,
+        help="Path to the directory containing test .inpt files."
+    )
+    parser.add_argument(
+        "parameters_json",
+        type=str,
+        help="Path to the parameters.json file."
+    )
+
+    args = parser.parse_args()
+
+    # Run the check
+    success = check_missing_parameters(args.test_directory,
+                                       args.parameters_json)
+    if not success:
+        exit(1)
+    else:
+        exit(0)
+if __name__ == "__main__":
+    main()

.github/workflows/test-outdated-package.py

@@ -0,0 +1,108 @@
+"""Test script to check if SPARC package version is older than
+the latest Changelog entry
+
+We generally do not check the other way around since sometimes a trivial bump of SPARC version may be necessary
+"""
+import re
+import json
+from datetime import datetime
+from pathlib import Path
+
+
+def load_parameters_json(json_path):
+    """
+    Load the parameters from the parameters.json file.
+    """
+    with open(json_path, 'r') as f:
+        parameters = json.load(f)
+    if "sparc_version" not in parameters:
+        raise KeyError("The 'sparc_version' field is missing in parameters.json")
+    return parameters["sparc_version"]
+
+
+def extract_latest_date_from_changelog(changelog_path):
+    """
+    Extracts the latest date from the changelog file.
+    """
+    date_patterns = [
+        r"(?P<date>\b(?:Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec) \d{1,2}, \d{4})",
+        r"(?P<date>\b(?:January|February|March|April|May|June|July|August|September|October|November|December) \d{1,2}, \d{4})",
+    ]
+
+    latest_date = None
+    changelog_path = Path(changelog_path)
+
+    with changelog_path.open("r") as f:
+        content = f.read()
+
+    for pattern in date_patterns:
+        matches = re.findall(pattern, content)
+        for match in matches:
+            try:
+                # Convert matched date to datetime object
+                parsed_date = datetime.strptime(match, "%b %d, %Y") if "," in match else datetime.strptime(match, "%B %d, %Y")
+                if latest_date is None or parsed_date > latest_date:
+                    latest_date = parsed_date
+            except ValueError:
+                continue  # Skip invalid date formats
+
+    if latest_date is None:
+        raise ValueError("No valid date found in the changelog.")
+    return latest_date
+
+
+def check_version_against_changelog(parameters_json_path, changelog_path):
+    """
+    Check if the package version in parameters.json is older than the latest changelog date.
+    """
+    # Load sparc_version from parameters.json
+    sparc_version = load_parameters_json(parameters_json_path)
+    version_date = datetime.strptime(sparc_version, "%Y.%m.%d")
+
+    # Extract the latest date from the changelog
+    latest_changelog_date = extract_latest_date_from_changelog(changelog_path)
+
+    if version_date < latest_changelog_date:
+        print("Version Check Report:")
+        print("-" * 60)
+        print(f"ERROR: SPARC version ({version_date.strftime('%Y.%m.%d')}) "
+              f"is older than the latest changelog date ({latest_changelog_date.strftime('%Y.%m.%d')}).")
+        print("Please update initialization.c!")
+        print("-" * 60)
+        return False
+    else:
+        print("Version Check Report:")
+        print("-" * 60)
+        print("SUCCESS:")
+        print("-" * 60)
+        return True
+
+
+def main():
+    import argparse
+    parser = argparse.ArgumentParser(
+        description="Check if package version is up-to-date with the changelog."
+    )
+    parser.add_argument(
+        "parameters_json",
+        type=str,
+        help="Path to the parameters.json file."
+    )
+    parser.add_argument(
+        "changelog",
+        type=str,
+        help="Path to the changelog file."
+    )
+
+    args = parser.parse_args()
+
+    # Run the version check
+    success = check_version_against_changelog(args.parameters_json, args.changelog)
+    if not success:
+        exit(1)
+    else:
+        exit(0)
+
+
+if __name__ == "__main__":
+    main()

.github/workflows/update-doc-pdf.yml

@@ -0,0 +1,90 @@
+name: Check and render LaTeX doc into pdf
+
+on: 
+  push:
+    branches:
+      - master
+    paths:
+      - doc/**
+      - .github/workflows/update-doc-pdf.yml
+  pull_request:
+    branches:
+      - master
+    paths:
+      - doc/**
+      - .github/workflows/update-doc-pdf.yml
+  workflow_dispatch:
+
+jobs:
+  check-parameters:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/checkout@v4
+    - uses: conda-incubator/setup-miniconda@v3
+      with:
+        python-version: "3.11"
+        activate-environment: sparc-test
+        conda-build-version: "24.9.0"
+        miniforge-version: latest # Fix according to https://github.com/conda-incubator/setup-miniconda?tab=readme-ov-file#example-10-miniforge
+        channels: conda-forge,defaults
+        channel-priority: true
+    - name: Install SPARC-X-API stable version for docparser
+      run: |
+        mamba install -c conda-forge pip setuptools
+        pip install git+https://github.com/SPARC-X/[email protected]
+    - name: Convert parameters.json
+      run: |
+        python -m sparc.docparser --include-subdirs doc/.LaTeX
+    - name: Check missing parameters in test examples
+      run: |
+        # Usage:
+        # python test-missing-parameters.py <test-dir> <parameters.json>
+        # If test fails, a list of missing / typo params will
+        # be written in output
+        python .github/workflows/test-missing-parameters.py \
+               tests/ ./parameters.json
+      
+  render-pdf-linux:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    needs: check-parameters
+    steps:
+    - uses: actions/checkout@v4
+    - uses: conda-incubator/setup-miniconda@v3
+      with:
+        python-version: "3.11"
+        activate-environment: sparc-test
+        conda-build-version: "24.9.0"
+        miniforge-version: latest # Fix according to https://github.com/conda-incubator/setup-miniconda?tab=readme-ov-file#example-10-miniforge
+        channels: conda-forge,defaults
+        channel-priority: true
+    - name: Install tectonic as latex rendering engine
+      run: |
+        mamba install -c conda-forge tectonic
+    - name: Make temp build dir
+      run: |
+        mkdir -p doc/_build
+    - name: Render main manual
+      run: |
+        tectonic -X compile doc/.LaTeX/Manual.tex \
+                 --outdir doc/_build
+        ls -al doc/_build
+    - name: Render subdir manuals
+      run: |
+        for dir in doc/.LaTeX/*; do
+          if [ -d "$dir" ]; then
+            manual=$(find "$dir" -maxdepth 1 -name "*Manual.tex" | head -n 1)
+            if [ -n "$manual" ]; then
+              tectonic -X compile "$manual" \
+                       --outdir doc/_build
+              echo "Rendered: $manual"
+            fi
+          fi
+        done
+        ls -al doc/_build
+        

ChangeLog

@@ -2,6 +2,15 @@
 -Date
 -Name
 -changes
+--------------
+Nov 23, 2024
+Name: Tian Tian
+Changes: (doc, CI workflow)
+1. Fix typo in SQ LaTeX doc
+2. Add CI workflow to check missing parameters
+3. Add CI workflow to validate and render LaTeX doc
+4. Add CI workflow to check outdated initialization.c (SPARC version) if older than current Changelog
+
 --------------
 Nov 18, 2024
 Name: Tian Tian, Lucas Timmerman

doc/.LaTeX/Introduction.tex

@@ -46,6 +46,8 @@
     \begin{itemize}
         \item \textbf{Benjamin Comer}: Code testing, Initial testing framework
         \item \textbf{Sushree Jagriti Sahoo}: Code testing
+        \item \textbf{Tian Tian}: Socket communication layer, code testing, Python API
+        \item \textbf{Lucas R Timmerman}: Socket communication layer, code testing, Python API
     \end{itemize}
  	\end{itemize}
 
@@ -416,6 +418,14 @@
   \begin{block}{Orbital Free DFT}
   \hyperlink{OFDFT_FLAG}{\texttt{OFDFT\_FLAG}} $\vert$ \hyperlink{TOL_OFDFT}{\texttt{TOL\_OFDFT}} $\vert$ \hyperlink{OFDFT_LAMBDA}{\texttt{OFDFT\_LAMBDA}}
   \end{block}
+
+  \begin{block}{Socket communication}
+  \hyperlink{SOCKET_FLAG}{\texttt{SOCKET\_FLAG}} $\vert$
+  \hyperlink{SOCKET_HOST}{\texttt{SOCKET\_HOST}} $\vert$
+  \hyperlink{SOCKET_PORT}{\texttt{SOCKET\_PORT}} $\vert$
+  \hyperlink{SOCKET_INET}{\texttt{SOCKET\_INET}} $\vert$
+  \hyperlink{SOCKET_MAX_NITER}{\texttt{SOCKET\_MAX\_NITER}} $\vert$
+  \end{block}
 
   \end{frame}