Convert command line interface to click

.github/workflows/executable.yml

@@ -0,0 +1,38 @@
+name: Standalone Executable
+
+on:
+  push:
+    branches:
+    - executable
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  build_wheels:
+    name: Build executable 📦 for windows
+    runs-on: windows-latest
+    steps:
+      - name: Harden Runner
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
+        with:
+          egress-policy: audit
+
+      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
+
+      - name: Set up Python
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
+        with:
+          python-version: 3.11
+
+      - name: Install development dependencies
+        run: |
+          python3 -m pip install -r requirements-exe.txt
+          python3 setup.py build_ext -i
+          python3 setup.py py2exe >> $GITHUB_STEP_SUMMARY
+
+      - uses: actions/upload-artifact@604373da6381bf24206979c74d06a550515601b9 # v4.4.1
+        with:
+          name: standalone
+          path: dist/*.exe

docs/conf.py

@@ -40,7 +40,7 @@
     "sphinx.ext.intersphinx",
     "sphinx.ext.githubpages",
     "sphinx_design",
-    "sphinxarg.ext",
+    "sphinx_click",
     "sphinxcontrib.bibtex",
 ]
 

docs/requirements.txt

@@ -4,4 +4,4 @@ sphinx_design==0.6.1
 sphinxcontrib-bibtex==2.6.3
 breathe==4.35.0
 exhale==0.3.7
-sphinx-argparse==0.5.2
+sphinx-click==6.0.0

docs/um/running-sansmic.rst

@@ -5,21 +5,12 @@ The following include all available output options, but note that not all option
 available if you have not installed the appropriate packages (see Advanced Installation).
 
 
-``sansmic``
------------
-
-.. argparse::
-   :module: sansmic.app
-   :func: _main_parser
+.. _sansmic:
+.. click:: sansmic.app:run
    :prog: sansmic
 
 
 
-
-``sansmic-convert``
--------------------
-
-.. argparse::
-   :module: sansmic.app
-   :func: _convert_parser
+.. _sansmic-convert:
+.. click:: sansmic.app:convert
    :prog: sansmic-convert

examples/basic.ipynb

@@ -13,7 +13,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -57,7 +57,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -77,7 +77,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -109,7 +109,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -133,7 +133,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -149,7 +149,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -244,7 +244,7 @@
     "## Running from the command line\n",
     "Jupyter is not a great way to demonstrate how to run sansmic from the command line; however, it is still possible to do so. The following code simulates the execution of the following command:\n",
     "\n",
-    "``sansmic old.dat -o cmdlineTest --no-json --no-hdf``\n",
+    "``sansmic old.dat -o cmdlineTest --no-hdf``\n",
     "\n",
     "Try adding \"-v\" or \"-vv\" at the end of the list to see the difference."
    ]
@@ -258,16 +258,14 @@
     "import sansmic.app\n",
     "\n",
     "\n",
-    "\n",
-    "resultsCmdLine = sansmic.app.main(\n",
+    "resultsCmdLine = sansmic.app.run(\n",
     "    [\n",
     "        \"old.dat\",\n",
     "        \"-o\",\n",
     "        \"cmdlineTest\",\n",
-    "        \"--no-json\",\n",
     "        \"--no-hdf\",\n",
     "    ],\n",
-    "    ret=True,\n",
+    "    standalone_mode=False,\n",
     ")"
    ]
   },
@@ -294,7 +292,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [

pyproject.toml

@@ -9,7 +9,7 @@ authors = [
     { name = "SANSMIC Authors (see AUTHORS.md)" },
 ]
 maintainers = [{ name = "David Hart", email = "[email protected]" }]
-dependencies = ["numpy", "pandas", 'tomli; python_version < "3.11"']
+dependencies = ["numpy", "pandas", 'tomli; python_version < "3.11"', "click"]
 classifiers = [
     "Development Status :: 4 - Beta",
     "License :: OSI Approved :: BSD License",
@@ -47,7 +47,7 @@ docs = [
     'sphinxcontrib-bibtex',
     'breathe',
     'exhale',
-    'sphinx-argparse',
+    'sphinx-click',
 ]
 
 [project.urls]
@@ -56,7 +56,7 @@ Issues = "https://github.com/sandialabs/sansmic/issues"
 Repository = "https://github.com/sandialabs/sansmic.git"
 
 [project.scripts]
-sansmic = "sansmic.app:main"
+sansmic = "sansmic.app:run"
 sansmic-convert = "sansmic.app:convert"
 
 [build-system]
@@ -124,11 +124,11 @@ default = "semantic-release <semantic-release>"
 [tool.semantic_release.commit_parser_options]
 allowed_tags = [
     # Non-source code changes (no change to version; omit from CHANGELOG by default)
-    "build",    # Changes to build system or external dependencies (omit from CHANGELOG - manually add if needed)
-    "ci",       # Changes to CI configuration files and scripts (omit from CHANGELOG - manually add if needed)
-    "chore",    # Other changes that don't touch the source code (omit from CHANGELOG - manually add if needed)
+    "build", # Changes to build system or external dependencies (omit from CHANGELOG - manually add if needed)
+    "ci",    # Changes to CI configuration files and scripts (omit from CHANGELOG - manually add if needed)
+    "chore", # Other changes that don't touch the source code (omit from CHANGELOG - manually add if needed)
     # Changes to test suites (no change to version; include in CHANGELOG by default)
-    "test",     # Adding missing tests or correcting existing tests (does not change package code)
+    "test", # Adding missing tests or correcting existing tests (does not change package code)
     # Changes to source code (possible change to version; include in CHANGELOG by default)
     "fix",      # A bug fix (a patch-level version change)
     "perf",     # A code change that improves performance (at-least patch-level, possibly minor version change)

requirements-exe.txt

@@ -0,0 +1,13 @@
+pip==24.2
+numpy==2.1.2
+pandas==2.2.3
+pybind11==2.13.6
+setuptools==75.1.0
+pyyaml==6.0.2
+nbmake==1.5.4
+h5py==3.12.1
+openpyxl==3.1.5
+tabulate==0.9.0
+lasio==0.31
+click==8.1.7
+py2exe==0.13.0.2

requirements.txt

@@ -2,3 +2,4 @@ numpy==2.1.2
 pandas==2.2.3
 pybind11==2.13.6
 setuptools==75.1.0
+click==8.1.7