ci: more more coverage

.dev.info

@@ -0,0 +1,12 @@
+
+Configuration for debugging
+:
+    {
+        "name": "Python: Debug Tests",
+        "type": "python",
+        "request": "launch",
+        "program": "${file}",
+        "purpose": ["debug-test"],
+        "console": "integratedTerminal",
+        "env": {"PYTEST_ADDOPTS": "--no-cov"}
+    }

CHANGELOG.rst

@@ -9,6 +9,11 @@ New features:
 
 Changes:
 
+* removed other_keys syntax
+* move all test data somewhere
+* removed smart naming of isotherm parameters
+* branches are internally 0,1 instead of false/true
+
 * Isotherm ``material`` and ``adsorbate`` are now always instantiated as
   ``pygaps.Material`` and ``pygaps.Adsorbate`` classes.
 * Added a "zero" thickness model that assumes no mono/multilayer sorption.

ci/templates/tox.ini

@@ -36,6 +36,7 @@ usedevelop =
 deps =
     pytest
     cover: coverage[toml]
+    cover: tomlkit
     cover: pytest-cov
 commands =
     cover: python setup.py clean --all build_ext --force --inplace

docs/conf.py

@@ -1,5 +1,5 @@
-# -*- coding: utf-8 -*-
-from __future__ import unicode_literals
+"""Configuration for documentation building"""
+# -- Init -----------------------------------------------------
 
 import os
 import sys
@@ -12,6 +12,7 @@
     html_theme = 'sphinx_rtd_theme'
 
 
+# -- Mocking of modules -----------------------------------------------------
 # Need to mock modules using MagicMock, as they won't be able to
 # be installed on readthedocs
 class Mock(MagicMock):
@@ -57,7 +58,7 @@ def __getattr__(cls, name):
 ]
 # If currently spellchecking
 if os.getenv('SPELLCHECK'):
-    extensions += 'sphinxcontrib.spelling',
+    extensions += 'sphinxcontrib.spelling'
     spelling_show_suggestions = True
     spelling_lang = 'en_US'
 
@@ -71,7 +72,7 @@ def __getattr__(cls, name):
 project = 'pygaps'
 year = '2021'
 author = 'Paul Iacomi'
-copyright = '{0}, {1}'.format(year, author)
+copyright = f'{year}, {author}'
 try:
     from importlib.metadata import version as imp_version
     version = release = imp_version("pygaps")
@@ -83,14 +84,19 @@ def __getattr__(cls, name):
 templates_path = ['.']
 
 # Needed for jupyter notebook compilation by nbsphinx
-exclude_patterns = ['_build', '**.ipynb_checkpoints']
+exclude_patterns = [
+    '_build',
+    '**.ipynb_checkpoints',
+]
 
 # Needed for jupyter notebook compilation by nbsphinx
 pygments_style = 'trac'
 
 # Suppressing the nonlocal_uri image warning, as it appears due to
 # github badges being stored on another server
-suppress_warnings = ['image.nonlocal_uri']
+suppress_warnings = [
+    'image.nonlocal_uri',
+]
 
 # External links
 extlinks = {

docs/examples/import.ipynb

@@ -17,7 +17,7 @@
    "source": [
     "from pathlib import Path\n",
     "import matplotlib.pyplot as plt\n",
-    "import pygaps\n",
+    "import pygaps.parsing as pgp \n",
     "\n",
     "json_path = Path.cwd() / 'data'"
    ]
@@ -40,8 +40,8 @@
    "metadata": {},
    "outputs": [
     {
-     "output_type": "stream",
      "name": "stdout",
+     "output_type": "stream",
      "text": [
       "Selected 5 isotherms with nitrogen at 77K\n"
      ]
@@ -52,7 +52,7 @@
     "isotherms_n2_77k_paths = list(Path(json_path / 'characterisation').rglob(\"*.json\" ))\n",
     "isotherms_n2_77k = []\n",
     "for filepath in isotherms_n2_77k_paths:\n",
-    "    isotherms_n2_77k.append(pygaps.isotherm_from_json(filepath))\n",
+    "    isotherms_n2_77k.append(pgp.isotherm_from_json(filepath))\n",
     "        \n",
     "print('Selected', len(isotherms_n2_77k), 'isotherms with nitrogen at 77K')"
    ]
@@ -63,8 +63,8 @@
    "metadata": {},
    "outputs": [
     {
-     "output_type": "stream",
      "name": "stdout",
+     "output_type": "stream",
      "text": [
       "Selected 2 room temperature calorimetry isotherms\n"
      ]
@@ -75,7 +75,7 @@
     "isotherms_calorimetry_paths = list(Path(json_path / 'calorimetry').rglob(\"*.json\" ))\n",
     "isotherms_calorimetry = []\n",
     "for filepath in isotherms_calorimetry_paths:\n",
-    "    isotherms_calorimetry.append(pygaps.isotherm_from_json(filepath))\n",
+    "    isotherms_calorimetry.append(pgp.isotherm_from_json(filepath))\n",
     "        \n",
     "print('Selected', len(isotherms_calorimetry), 'room temperature calorimetry isotherms')"
    ]
@@ -86,8 +86,8 @@
    "metadata": {},
    "outputs": [
     {
-     "output_type": "stream",
      "name": "stdout",
+     "output_type": "stream",
      "text": [
       "Selected 2 isotherms for IAST calculation\n"
      ]
@@ -98,7 +98,7 @@
     "isotherms_iast_paths = list(Path(json_path / 'iast').rglob(\"*.json\" ))\n",
     "isotherms_iast = []\n",
     "for filepath in isotherms_iast_paths:\n",
-    "    isotherms_iast.append(pygaps.isotherm_from_json(filepath))\n",
+    "    isotherms_iast.append(pgp.isotherm_from_json(filepath))\n",
     "        \n",
     "print('Selected', len(isotherms_iast), 'isotherms for IAST calculation')"
    ]
@@ -109,8 +109,8 @@
    "metadata": {},
    "outputs": [
     {
-     "output_type": "stream",
      "name": "stdout",
+     "output_type": "stream",
      "text": [
       "Selected 3 isotherms for isosteric enthalpy calculation\n"
      ]
@@ -121,7 +121,7 @@
     "isotherms_isosteric_paths = list(Path(json_path / 'isosteric').rglob(\"*.json\" ))\n",
     "isotherms_isosteric = []\n",
     "for filepath in isotherms_isosteric_paths:\n",
-    "    isotherms_isosteric.append(pygaps.isotherm_from_json(filepath))\n",
+    "    isotherms_isosteric.append(pgp.isotherm_from_json(filepath))\n",
     "        \n",
     "print('Selected', len(isotherms_isosteric), 'isotherms for isosteric enthalpy calculation')"
    ]
@@ -148,4 +148,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}

docs/manual/isotherm.rst

@@ -166,8 +166,8 @@ calorimetry data, magnetic field strengths, or other simultaneous measurements.
 
 If a DataFrame is used, ``loading_key`` and ``pressure_key`` are required
 parameters specifying which column in the DataFrame contains what data of the
-isotherm. If other columns are to be stored in the isotherm object, their names
-should be passed in a list as the ``other_keys`` parameter. As an example:
+isotherm. Other columns in the dataframe are also stored in the isotherm object.
+As an example:
 
 ::
 
@@ -185,8 +185,6 @@ should be passed in a list as the ``other_keys`` parameter. As an example:
 
         loading_key='loading',          # The loading column
         pressure_key='pressure',        # The pressure column
-        other_keys=['enthalpy',
-                    'xrd_peak_1'],      # The columns containing the other data
 
         # Other required isotherm parameters
 

tox.ini

@@ -40,6 +40,7 @@ usedevelop =
 deps =
     pytest
     cover: coverage[toml]
+    cover: tomlkit
     cover: pytest-cov
 commands =
     cover: python setup.py clean --all build_ext --force --inplace