Merge branch 'dev' of github.com:johbackm/PySP2 into dev

.github/workflows/pypi-release.yml

@@ -0,0 +1,74 @@
+name: Build and Upload PySP2 Release to PyPI
+on:
+  release:
+    types:
+      - published
+
+jobs:
+  build-artifacts:
+    runs-on: ubuntu-latest
+    if: github.repository == 'ARM-DOE/PySP2'
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v4
+        name: Install Python
+        with:
+          python-version: 3.11
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install setuptools setuptools-scm wheel twine check-manifest
+      - name: Build tarball and wheels
+        run: |
+          git clean -xdf
+          git restore -SW .
+          python -m build --sdist --wheel .
+      - name: Check built artifacts
+        run: |
+          python -m twine check dist/*
+          pwd
+          if [ -f dist/pysp2-0.0.0.tar.gz ]; then
+            echo "❌ INVALID VERSION NUMBER"
+            exit 1
+          else
+            echo "✅ Looks good"
+          fi
+      - uses: actions/upload-artifact@v3
+        with:
+          name: releases
+          path: dist
+
+  test-built-dist:
+    needs: build-artifacts
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/setup-python@v4
+        name: Install Python
+        with:
+          python-version: "3.x"
+      - uses: actions/download-artifact@v3
+        with:
+          name: releases
+          path: dist
+      - name: List contents of built dist
+        run: |
+          ls -ltrh
+          ls -ltrh dist
+  upload-to-pypi:
+    needs: test-built-dist
+    if: github.event_name == 'release'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: releases
+          path: dist
+      - name: Publish package to PyPI
+        uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}
+          verbose: true

docs/environment_docs.yml

@@ -5,10 +5,11 @@ channels:
 dependencies:
   - act-atmos
   - xarray
+  - sphinx
+  - pydata-sphinx-theme
   - pip:
-      - sphinx
       - sphinx_gallery
       - sphinx-copybutton
-      - pydata-sphinx-theme<0.9.0
       - sphinx_design
       - nbsphinx
+      - sphinxcontrib-applehelp<1.0.8

docs/source/_static/doc_shared.js

@@ -1,4 +1,4 @@
-const project = "ACT";
+const project = "PySP2";
 
 // Borrowed from Bokeh docs to look for a banner.html at the base of the docs repo and add that
 // to the banner if present.

docs/source/_templates/layout.html

@@ -6,12 +6,3 @@
 </style>
     {{ super() }}
 {% endblock %}
-
-{% block docs_navbar %}
-  <nav class="navbar navbar-dark navbar-expand-lg bg-arm fixed-top bd-navbar shadow" id="navbar-main">
-    {%- include "docs-navbar.html" %}
-  </nav>
-
-{# Added to support a banner with an alert #}
-    <div class="container-fluid" id="banner"></div>
-{% endblock %}

docs/source/conf.py

@@ -72,9 +72,6 @@
 napoleon_include_init_with_doc = False
 napoleon_use_param = False
 
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
@@ -87,7 +84,7 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
 
-html_css_files = ['default.css']
+html_css_files = ['act-theme.css']
 
 html_js_files = ['doc_shared.js']
 

pysp2/__init__.py

@@ -9,4 +9,4 @@
 from . import vis
 from . import testing
 
-__version__ = "1.3.3"
+__version__ = "1.4.0"

pysp2/io/read_hk.py

@@ -26,7 +26,12 @@ def read_hk_file(file_name):
     hk_df: pandas.DataFrame
         The housekeeping information in a pandas DataFrame
     """
-    my_df = act.io.read_csv(file_name, sep="\t")
+
+    try:
+        my_df = act.io.csvfiles.read_csv(file_name, sep="\t")
+    except AttributeError:
+        my_df = act.io.text.read_csv(file_name, sep="\t")
+
     # Parse time from filename
     start_time = pd.Timestamp('1904-01-01')
     my_df = my_df.rename({'index': 'time'}) 

pysp2/vis/plot_wave.py

@@ -50,9 +50,9 @@ def plot_wave(ds, record_no, chn, plot_fit=True,
         if append_to_display is not False:
             display = append_to_display
         else:
-            display = act.plotting.HistogramDisplay(inp_data)
+            display = act.plotting.DistributionDisplay(inp_data)
     else:
-        display = act.plotting.HistogramDisplay(inp_data, **init_kwargs)
+        display = act.plotting.DistributionDisplay(inp_data, **init_kwargs)
     if 'subplot_index' in kwargs.keys():
         ax = display.plot_size_distribution(
             'Data_ch' + str(chn), bins,

setup.py

@@ -40,8 +40,8 @@
 LICENSE = 'BSD'
 PLATFORMS = "Linux, Windows, OSX"
 MAJOR = 1
-MINOR = 3
-MICRO = 4
+MINOR = 4
+MICRO = 0
 
 #SCRIPTS = glob.glob('scripts/*')
 #TEST_SUITE = 'nose.collector'

tests/test_gfit.py

@@ -29,8 +29,7 @@ def test_psds():
         my_binary['ScatDiaBC50'].values[ScatRejectKey == 0]) < 1000.
     my_psds = pysp2.util.process_psds(my_binary, my_hk, my_ini)
     np.testing.assert_almost_equal(my_psds['NumConcIncan'].max(), 0.95805343)
-    np.testing.assert_almost_equal(my_binary['DeadtimeRelativeBias'].mean(), -0.00023515)
-    coeff, beam_profile = pysp2.util.beam_shape(my_binary,beam_position_from='peak maximum',Globals=pysp2.util.DMTGlobals())
-
-
-
+    np.testing.assert_almost_equal(my_psds['ScatNumEnsemble'].sum(), 254.773995310)
+    np.testing.assert_almost_equal(my_psds['IncanNumEnsemble'].sum(), 32.22939087)
+    np.testing.assert_almost_equal(my_psds['ScatMassEnsemble'].sum(), 3.15026266)
+    np.testing.assert_almost_equal(my_psds['IncanMassEnsemble'].sum(), 0.08177226)