Tutorials as git subtree for tutorials with nbsphinx

docs/source/conf.py

@@ -58,7 +58,10 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = []
+exclude_patterns = [
+    "getting_started/tutorials/tutorials_repo/README.rst",
+    "getting_started/tutorials/tutorials_repo/demos",
+]
 
 
 # -- Options for HTML output -------------------------------------------------

docs/source/developing/index.rst

@@ -133,6 +133,17 @@ And then run command for testing with ``--external`` option::
     pytest tests --external
 
 
+Maintaining a copy of the tutorials with ``git subtree``
+********************************************************
+
+The tutorials for ixdat is developed in a
+`separate repository <https://github.com/ixdat/tutorials>`_. But these tutorials are copied into
+the ixdat repository in order to be able to generate docs from the Jupyter notebooks. This copy
+is maintained via a git feature called ``git subtree``. The copy of the tutorials in ixdat can
+be updated with new changes with the following command::
+
+    git subtree pull --prefix docs/source/getting_started/tutorials/tutorials_repo https://github.com/ixdat/tutorials.git main --squash
+
 Write to us
 ***********
 We'd love to know what you're working on and help with any issues developing, even

docs/source/getting_started/tutorials/index.rst

@@ -67,7 +67,7 @@ https://github.com/ixdat/tutorials/blob/main/L1_basic_concepts/01_Readers.ipynb
 .. toctree::
     :maxdepth: 1
 
-    L1_basic_concepts/01_readers.ipynb
+    tutorials_repo/L1_basic_concepts/01_Readers.ipynb
 
 
 .. _ec_tutorials:
@@ -79,7 +79,7 @@ https://github.com/ixdat/tutorials/blob/main/L2_techniques/electrochemistry/02_c
 .. toctree::
     :maxdepth: 1
 
-    L2_techniques/electrochemistry/02_comparing_cycles
+    tutorials_repo/L2_techniques/electrochemistry/02_comparing_cycles
 
 
 .. _ecms_tutorial:
@@ -91,7 +91,7 @@ https://github.com/ixdat/tutorials/blob/main/L2_techniques/ec_ms_quantification/
 .. toctree::
     :maxdepth: 1
 
-    L2_techniques/ec_ms_quantification/EC-MS_ixdat_tutorial
+    tutorials_repo/ec_ms_quantification/EC-MS_ixdat_tutorial
 
 .. _sec_tutorial:
 
@@ -102,7 +102,7 @@ https://github.com/ixdat/tutorials/blob/main/L2_techniques/spectroelectrochemist
 .. toctree::
     :maxdepth: 1
 
-    L2_techniques/spectroelectrochemistry/spectroelectrochemistry_demo
+    tutorials_repo/L2_techniques/spectroelectrochemistry/spectroelectrochemistry_demo
 
 
 .. _data_tutorial:
@@ -114,7 +114,7 @@ https://github.com/ixdat/tutorials/blob/main/L3_data_structure/01_reading_and_us
 .. toctree::
     :maxdepth: 1
 
-    L3_data_structure/01_reading_and_using_data
+    tutorials_repo/L3_data_structure/01_reading_and_using_data
 
 
 This repository is a bit of a mess at the moment, apologies, but the tutorials themselves are

docs/source/getting_started/tutorials/tutorials_repo/.gitignore

@@ -0,0 +1,139 @@
+# pycharm
+.idea/
+
+# data
+data/
+
+# renderings
+*.png
+*.jpg
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

docs/source/getting_started/tutorials/L2_techniques/ec_ms_quantification/make_calibration.py → docs/source/getting_started/tutorials/tutorials_repo/L2_techniques/ec_ms_quantification/make_calibration.py

@@ -6,10 +6,7 @@
 from pathlib import Path
 
 
-data_dir = (
-    Path.home()
-    / "Dropbox/ixdat_resources/presentations_and_workshops/22K16_ICL_quant/2022-09-27 21_15_42 22I27_London"
-)
+data_dir = Path.home() / "Dropbox/ixdat_resources/presentations_and_workshops/22K16_ICL_quant/2022-09-27 21_15_42 22I27_London"
 
 for f in data_dir.iterdir():
     print(f)
@@ -37,33 +34,41 @@
     n_el=-2,
     tspan_bg=[50, 100],
     selector_list=[2, 5, 8],
-    t_steady_pulse=30,
+    t_steady_pulse=30
 )
 cal_O2_M32_EC = ecms.ecms_calibration_curve(
     mol="O2",
     mass="M32",
     n_el=4,  # 2 H2O --> O2 + 4 (H+ + e-)
     tspan_bg=[50, 100],
     selector_list=[10, 12, 14],
-    t_steady_pulse=30,
+    t_steady_pulse=30
 )
 cal_CO2_M44_EC = ecms.ecms_calibration_curve(
     mol="CO2",
     mass="M44",
     n_el=2,
     tspan_bg=[2520, 2540],
     selector_list=[28, 32, 34],
-    t_steady_pulse=30,
+    t_steady_pulse=30
 )
 
-cal_He = ecms.gas_flux_calibration(mol="He", mass="M4", tspan=[0, 50])
-cal_CO = ecms.gas_flux_calibration(mol="CO", mass="M28", tspan=[2800, 2850])
+cal_He = ecms.gas_flux_calibration(
+    mol="He",
+    mass="M4",
+    tspan=[0, 50]
+)
+cal_CO = ecms.gas_flux_calibration(
+    mol="CO",
+    mass="M28",
+    tspan=[2800, 2850]
+)
 
 cal_air = ms.multicomp_gas_flux_calibration(
     mol_list=["N2", "O2", "Ar"],
     mass_list=["M28", "M32", "M40"],
     gas={"N2": 0.79, "O2": 0.20, "Ar": 0.01},
-    tspan=[7100, 7200],
+    tspan=[7100, 7200]
 )
 
 from ixdat.si_quant_patch import append_sensitivity_factors
@@ -78,5 +83,7 @@
 ax.get_figure().savefig("calibration_trend.png")
 
 
-ecms.set_quantifier(calibration=calibration, mol_list=["CO2"], mass_list=["M44"])
-ecms.export(mol_list=["CO2"], mass_list=["M44"])
+ecms.set_quantifier(
+    calibration=calibration, mol_list=["CO2"], mass_list=["M44"]
+)
+ecms.export(mol_list=["CO2"], mass_list=["M44"])

docs/source/getting_started/tutorials/L2_techniques/electrochemistry/02_comparing_cycles.ipynb → docs/source/getting_started/tutorials/tutorials_repo/L2_techniques/electrochemistry/02_comparing_cycles.ipynb

@@ -57,7 +57,7 @@
     "# co_strip = CyclicVoltammagram.read(d\"../loading_appending_and_saving/co_strip.csv\", reader=\"ixdat\")\n",
     "if True:  # Set this to False for offline work (requires you have downloaded the data file.)\n",
     "    co_strip = CyclicVoltammogram.read_url(\n",
-    "        \"https://raw.githubusercontent.com/ixdat/tutorials/main/L3_data_structure/exports/co_strip.csv\",\n",
+    "        \"https://raw.githubusercontent.com/ixdat/tutorials/main/electrochemistry/data/co_strip.csv\",\n",
     "        reader=\"ixdat\"\n",
     "    )\n",
     "else:\n",
@@ -452,7 +452,7 @@
     "# oxide_reduction = CyclicVoltammagram.read(data_directory / \"oxide_reduction.csv\", reader=\"ixdat\")\n",
     "if True:  # Set this to False for offline work (requires you have downloaded the data file.)\n",
     "    oxide_reduction = CyclicVoltammogram.read_url(\n",
-    "        \"https://raw.githubusercontent.com/ixdat/tutorials/main/L3_data_structure/exports/oxide_reduction.csv\",\n",
+    "        \"https://raw.githubusercontent.com/ixdat/tutorials/main/electrochemistry/data/oxide_reduction.csv\",\n",
     "        reader=\"ixdat\"\n",
     "    )\n",
     "else:\n",
@@ -477,7 +477,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -491,7 +491,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.7.4"
   }
  },
  "nbformat": 4,

docs/source/getting_started/tutorials/L2_techniques/exercise_answers/02a_analyze_oxide_reduction.py → docs/source/getting_started/tutorials/tutorials_repo/L2_techniques/exercise_answers/02a_analyze_oxide_reduction.py

@@ -14,7 +14,7 @@
 plt.close("all")
 
 meas = CV.read_url(
-    "https://raw.githubusercontent.com/ixdat/tutorials/main/L3_data_structure/exports/oxide_reduction.csv",
+    "https://raw.githubusercontent.com/ixdat/tutorials/main/electrochemistry/data/oxide_reduction.csv",
     reader="ixdat",
 )
 

docs/source/getting_started/tutorials/L3_data_structure/data/co_strip.csv → docs/source/getting_started/tutorials/tutorials_repo/L3_data_structure/exports/co_strip.csv

@@ -1,11 +1,11 @@
-ixdat version = 0.2.5
+ixdat version = 0.2.0dev
 name = extended_platinum_ec
 technique = EC
-tstamp = 1580476422.056785
+tstamp = 1580480022.056785
 backend_name = BackendBase(none, address=none)
-id = 8
+id = 7
 timecol 'time/s' for: '$U_{RHE}$ / [V]' and '<I>/mA' and 'selector'
-aliases = {"t": ["time/s"], "raw_potential": ["$U_{RHE}$ / [V]"], "raw_current": ["raw_current=0", "<I>/mA", "I/mA"], "cycle": ["cycle number"]}
+aliases = {"t": ["time/s"], "raw_potential": ["$U_{RHE}$ / [V]"], "raw_current": ["<I>/mA"], "selector": ["selector"]}
 N_header_lines = 11
 
 time/s,	$U_{RHE}$ / [V],	<I>/mA,	selector