deploy: d4fe8a3

JaGeo · Apr 21, 2024 · d21abdb · d21abdb
commit d21abdb
Show file tree

Hide file tree

Showing 367 changed files with 76,551 additions and 0 deletions.
diff --git a/.buildinfo b/.buildinfo
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: e115b12a6e1950854652473c17e39d56
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.doctrees/about/changelog.doctree b/.doctrees/about/changelog.doctree
diff --git a/.doctrees/about/license.doctree b/.doctrees/about/license.doctree
diff --git a/.doctrees/dev/contributing.doctree b/.doctrees/dev/contributing.doctree
diff --git a/.doctrees/dev/dev_installation.doctree b/.doctrees/dev/dev_installation.doctree
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/fundamentals/index.doctree b/.doctrees/fundamentals/index.doctree
diff --git a/.doctrees/index.doctree b/.doctrees/index.doctree
diff --git a/.doctrees/installation/index.doctree b/.doctrees/installation/index.doctree
diff --git a/.doctrees/reference/cli.doctree b/.doctrees/reference/cli.doctree
diff --git a/.doctrees/reference/cli_subcommands/createinputs.doctree b/.doctrees/reference/cli_subcommands/createinputs.doctree
diff --git a/.doctrees/reference/cli_subcommands/description.doctree b/.doctrees/reference/cli_subcommands/description.doctree
diff --git a/.doctrees/reference/cli_subcommands/descriptionquality.doctree b/.doctrees/reference/cli_subcommands/descriptionquality.doctree
diff --git a/.doctrees/reference/cli_subcommands/plot.doctree b/.doctrees/reference/cli_subcommands/plot.doctree
diff --git a/.doctrees/reference/cli_subcommands/plotauto.doctree b/.doctrees/reference/cli_subcommands/plotauto.doctree
diff --git a/.doctrees/reference/cli_subcommands/plotautoia.doctree b/.doctrees/reference/cli_subcommands/plotautoia.doctree
diff --git a/.doctrees/reference/cli_subcommands/plotdos.doctree b/.doctrees/reference/cli_subcommands/plotdos.doctree
diff --git a/.doctrees/reference/cli_subcommands/ploticohpdistance.doctree b/.doctrees/reference/cli_subcommands/ploticohpdistance.doctree
diff --git a/.doctrees/reference/index.doctree b/.doctrees/reference/index.doctree
diff --git a/.doctrees/reference/lobsterpy.cohp.analyze.Analysis.doctree b/.doctrees/reference/lobsterpy.cohp.analyze.Analysis.doctree
diff --git a/.doctrees/reference/lobsterpy.cohp.analyze.doctree b/.doctrees/reference/lobsterpy.cohp.analyze.doctree
diff --git a/.doctrees/reference/lobsterpy.cohp.describe.Description.doctree b/.doctrees/reference/lobsterpy.cohp.describe.Description.doctree
diff --git a/.doctrees/reference/lobsterpy.cohp.describe.doctree b/.doctrees/reference/lobsterpy.cohp.describe.doctree
diff --git a/.doctrees/reference/lobsterpy.cohp.doctree b/.doctrees/reference/lobsterpy.cohp.doctree
diff --git a/.doctrees/reference/lobsterpy.featurize.batch.BatchCoxxFingerprint.doctree b/.doctrees/reference/lobsterpy.featurize.batch.BatchCoxxFingerprint.doctree
diff --git a/.doctrees/reference/lobsterpy.featurize.batch.BatchDosFeaturizer.doctree b/.doctrees/reference/lobsterpy.featurize.batch.BatchDosFeaturizer.doctree
diff --git a/.doctrees/reference/lobsterpy.featurize.batch.BatchStructureGraphs.doctree b/.doctrees/reference/lobsterpy.featurize.batch.BatchStructureGraphs.doctree
diff --git a/.doctrees/reference/lobsterpy.featurize.batch.BatchSummaryFeaturizer.doctree b/.doctrees/reference/lobsterpy.featurize.batch.BatchSummaryFeaturizer.doctree
diff --git a/.doctrees/reference/lobsterpy.featurize.batch.doctree b/.doctrees/reference/lobsterpy.featurize.batch.doctree
diff --git a/.doctrees/reference/lobsterpy.featurize.core.CoxxFingerprint.doctree b/.doctrees/reference/lobsterpy.featurize.core.CoxxFingerprint.doctree
diff --git a/.doctrees/reference/lobsterpy.featurize.core.DosFingerprint.doctree b/.doctrees/reference/lobsterpy.featurize.core.DosFingerprint.doctree
diff --git a/.doctrees/reference/lobsterpy.featurize.core.FeaturizeCOXX.doctree b/.doctrees/reference/lobsterpy.featurize.core.FeaturizeCOXX.doctree
diff --git a/.doctrees/reference/lobsterpy.featurize.core.FeaturizeCharges.doctree b/.doctrees/reference/lobsterpy.featurize.core.FeaturizeCharges.doctree
diff --git a/.doctrees/reference/lobsterpy.featurize.core.FeaturizeDoscar.doctree b/.doctrees/reference/lobsterpy.featurize.core.FeaturizeDoscar.doctree
diff --git a/.doctrees/reference/lobsterpy.featurize.core.FeaturizeLobsterpy.doctree b/.doctrees/reference/lobsterpy.featurize.core.FeaturizeLobsterpy.doctree
diff --git a/.doctrees/reference/lobsterpy.featurize.core.doctree b/.doctrees/reference/lobsterpy.featurize.core.doctree
diff --git a/.doctrees/reference/lobsterpy.featurize.doctree b/.doctrees/reference/lobsterpy.featurize.doctree
diff --git a/.doctrees/reference/lobsterpy.featurize.utils.doctree b/.doctrees/reference/lobsterpy.featurize.utils.doctree
diff --git a/.doctrees/reference/lobsterpy.featurize.utils.get_file_paths.doctree b/.doctrees/reference/lobsterpy.featurize.utils.get_file_paths.doctree
diff --git a/.doctrees/reference/lobsterpy.featurize.utils.get_structure_path.doctree b/.doctrees/reference/lobsterpy.featurize.utils.get_structure_path.doctree
diff --git a/.doctrees/reference/lobsterpy.plotting.IcohpDistancePlotter.doctree b/.doctrees/reference/lobsterpy.plotting.IcohpDistancePlotter.doctree
diff --git a/.doctrees/reference/lobsterpy.plotting.InteractiveCohpPlotter.doctree b/.doctrees/reference/lobsterpy.plotting.InteractiveCohpPlotter.doctree
diff --git a/.doctrees/reference/lobsterpy.plotting.PlainCohpPlotter.doctree b/.doctrees/reference/lobsterpy.plotting.PlainCohpPlotter.doctree
diff --git a/.doctrees/reference/lobsterpy.plotting.PlainDosPlotter.doctree b/.doctrees/reference/lobsterpy.plotting.PlainDosPlotter.doctree
diff --git a/.doctrees/reference/lobsterpy.plotting.TYPE_CHECKING.doctree b/.doctrees/reference/lobsterpy.plotting.TYPE_CHECKING.doctree
diff --git a/.doctrees/reference/lobsterpy.plotting.base_style.doctree b/.doctrees/reference/lobsterpy.plotting.base_style.doctree
diff --git a/.doctrees/reference/lobsterpy.plotting.doctree b/.doctrees/reference/lobsterpy.plotting.doctree
diff --git a/.doctrees/reference/lobsterpy.plotting.get_style_list.doctree b/.doctrees/reference/lobsterpy.plotting.get_style_list.doctree
diff --git a/.doctrees/reference/lobsterpy.plotting.layout_dicts.cohp_axis_style_dict.doctree b/.doctrees/reference/lobsterpy.plotting.layout_dicts.cohp_axis_style_dict.doctree
diff --git a/.doctrees/reference/lobsterpy.plotting.layout_dicts.doctree b/.doctrees/reference/lobsterpy.plotting.layout_dicts.doctree
diff --git a/.doctrees/reference/lobsterpy.plotting.layout_dicts.energy_axis_style_dict.doctree b/.doctrees/reference/lobsterpy.plotting.layout_dicts.energy_axis_style_dict.doctree
diff --git a/.doctrees/reference/lobsterpy.plotting.layout_dicts.layout_dict.doctree b/.doctrees/reference/lobsterpy.plotting.layout_dicts.layout_dict.doctree
diff --git a/.doctrees/reference/lobsterpy.plotting.layout_dicts.legend_style_dict.doctree b/.doctrees/reference/lobsterpy.plotting.layout_dicts.legend_style_dict.doctree
diff --git a/.doctrees/reference/lobsterpy.plotting.layout_dicts.spin_down_trace_style_dict.doctree b/.doctrees/reference/lobsterpy.plotting.layout_dicts.spin_down_trace_style_dict.doctree
diff --git a/.doctrees/reference/lobsterpy.plotting.layout_dicts.spin_up_trace_style_dict.doctree b/.doctrees/reference/lobsterpy.plotting.layout_dicts.spin_up_trace_style_dict.doctree
diff --git a/.doctrees/reference/lobsterpy.structuregraph.doctree b/.doctrees/reference/lobsterpy.structuregraph.doctree
diff --git a/.doctrees/reference/lobsterpy.structuregraph.graph.LobsterGraph.doctree b/.doctrees/reference/lobsterpy.structuregraph.graph.LobsterGraph.doctree
diff --git a/.doctrees/reference/lobsterpy.structuregraph.graph.TYPE_CHECKING.doctree b/.doctrees/reference/lobsterpy.structuregraph.graph.TYPE_CHECKING.doctree
diff --git a/.doctrees/reference/lobsterpy.structuregraph.graph.doctree b/.doctrees/reference/lobsterpy.structuregraph.graph.doctree
diff --git a/.doctrees/tutorial/atomateauto.doctree b/.doctrees/tutorial/atomateauto.doctree
diff --git a/.doctrees/tutorial/commandlineinterface.doctree b/.doctrees/tutorial/commandlineinterface.doctree
diff --git a/.doctrees/tutorial/computingtimes.doctree b/.doctrees/tutorial/computingtimes.doctree
diff --git a/.doctrees/tutorial/index.doctree b/.doctrees/tutorial/index.doctree
diff --git a/.doctrees/tutorial/tutorial.doctree b/.doctrees/tutorial/tutorial.doctree
diff --git a/.nojekyll b/.nojekyll
diff --git a/_downloads/8f717a44707c0b40f1d30cb8055189c3/CdF2.html b/_downloads/8f717a44707c0b40f1d30cb8055189c3/CdF2.html
diff --git a/_downloads/bdff33f4f22a5d2dc65348c72950861a/CdF2_orb.html b/_downloads/bdff33f4f22a5d2dc65348c72950861a/CdF2_orb.html
diff --git a/_images/133c48c41599bd585642e03046f85842ed5a33dbb97061a89b16d1ec61e620d1.png b/_images/133c48c41599bd585642e03046f85842ed5a33dbb97061a89b16d1ec61e620d1.png
diff --git a/_images/27f976ef9fa80d145ce17d374cafe9649ab7eeb85c6b8416f43dd4f8119a297c.png b/_images/27f976ef9fa80d145ce17d374cafe9649ab7eeb85c6b8416f43dd4f8119a297c.png
diff --git a/_images/606677ab9c91a4053cd1e8baa19fc92fe0f24b974d824bd1e2723e5f44e166cd.png b/_images/606677ab9c91a4053cd1e8baa19fc92fe0f24b974d824bd1e2723e5f44e166cd.png
diff --git a/_images/COHP.png b/_images/COHP.png
diff --git a/_images/COHP_330.png b/_images/COHP_330.png
diff --git a/_images/COOP_330.png b/_images/COOP_330.png
diff --git a/_images/DOS_example.png b/_images/DOS_example.png
diff --git a/_images/ICOHP.png b/_images/ICOHP.png
diff --git a/_images/ICOHPs_distance_example.png b/_images/ICOHPs_distance_example.png
diff --git a/_images/LobsterEnv_schema.png b/_images/LobsterEnv_schema.png
diff --git a/_images/a8690f4f368df3a8ce5806f83bfc67c1426fc41044c6f155ce2abbcfd5cd0ab3.png b/_images/a8690f4f368df3a8ce5806f83bfc67c1426fc41044c6f155ce2abbcfd5cd0ab3.png
diff --git a/_images/bonding_percentage.png b/_images/bonding_percentage.png
diff --git a/_images/f7d0d317d167d62cf467a24a25093edeb9794ad4d5a7ffec62f3b0d1bc812182.png b/_images/f7d0d317d167d62cf467a24a25093edeb9794ad4d5a7ffec62f3b0d1bc812182.png
diff --git a/_images/orbital_wise_illustration.png b/_images/orbital_wise_illustration.png
diff --git a/_modules/index.html b/_modules/index.html
diff --git a/_modules/lobsterpy/cohp/analyze.html b/_modules/lobsterpy/cohp/analyze.html
diff --git a/_modules/lobsterpy/cohp/describe.html b/_modules/lobsterpy/cohp/describe.html
diff --git a/_modules/lobsterpy/featurize/batch.html b/_modules/lobsterpy/featurize/batch.html
diff --git a/_modules/lobsterpy/featurize/core.html b/_modules/lobsterpy/featurize/core.html
diff --git a/_modules/lobsterpy/featurize/utils.html b/_modules/lobsterpy/featurize/utils.html
diff --git a/_modules/lobsterpy/plotting.html b/_modules/lobsterpy/plotting.html
diff --git a/_modules/lobsterpy/structuregraph/graph.html b/_modules/lobsterpy/structuregraph/graph.html
diff --git a/_sources/about/changelog.md b/_sources/about/changelog.md
@@ -0,0 +1,2 @@
+```{include} ../../CHANGELOG.md
+```
diff --git a/_sources/about/license.md b/_sources/about/license.md
@@ -0,0 +1,32 @@
+License
+=======
+
+BSD 3-Clause License
+
+Copyright (c) 2021, LobsterPy Development Team
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/_sources/dev/contributing.md b/_sources/dev/contributing.md
@@ -0,0 +1,2 @@
+```{include} ../../CONTRIBUTING.md
+```
diff --git a/_sources/dev/dev_installation.md b/_sources/dev/dev_installation.md
@@ -0,0 +1,53 @@
+# Developer Installation
+
+Install LobsterPy from source, by cloning the repository via [github](https://github.com/JaGeo/LobsterPy.git)
+
+```bash
+git clone https://github.com/JaGeo/LobsterPy.git
+cd LobsterPy
+pip install -e .[featurizer,docs,tests,dev]
+```
+This will install LobsterPy will all dependencies for tests, pre-commit and docs building.
+
+## Running unit tests
+
+Unit tests can be run from the source folder using `pytest`. 
+
+```bash
+pytest
+```
+This will run all the tests.
+
+To get a detailed report of test coverage you can use following command
+```bash
+pytest --cov=lobsterpy --cov-report term-missing --cov-append
+```
+
+If you feel test execution takes too long locally, you can speedup the execution using [pytest-xdist](https://pypi.org/project/pytest-xdist/). Install this in library in your environment using
+
+```bash
+pip install pytest-xdist
+```
+
+Once installed, you can now use multiple processors to run your tests. For example, if you want to use 8 processors to run tests in parallel, run
+
+```bash
+pytest -n 8
+```
+
+We rely on pytest-split to run tests in parallel on github workflow, thus it is necessary to update the test-durations files in the repository, incase you add new tests. To generate this file, use
+
+```bash
+pytest --cov=lobsterpy --cov-append --splits 1 --group 1 --durations-path ./tests/test_data/.pytest-split-durations --store-durations
+```
+
+## Building the documentation locally
+
+The atomate2 documentation can be built using the sphinx package.
+
+The docs can be built to the `_build` directory:
+
+```bash
+sphinx-build -W docs _build
+```
+
diff --git a/_sources/fundamentals/index.ipynb b/_sources/fundamentals/index.ipynb
diff --git a/_sources/index.md b/_sources/index.md
@@ -0,0 +1,84 @@
+```{toctree}
+:caption: User Guide
+:hidden:
+installation/index
+fundamentals/index
+tutorial/index
+```
+
+```{toctree}
+:caption: Reference
+:hidden:
+reference/index
+reference/cli
+```
+
+```{toctree}
+:caption: Contributing Guide
+:hidden:
+dev/contributing
+dev/dev_installation
+```
+
+```{toctree}
+:caption: About
+:hidden:
+about/changelog
+about/license
+```
+
+# LobsterPy documentation
+
+**Date**: {sub-ref}`today`
+
+**Useful links**:
+[Github Repository](https://github.com/JaGeo/LobsterPy) |
+[PyPI](https://pypi.org/project/lobsterpy/) |
+[Issues & Ideas](https://github.com/JaGeo/LobsterPy/issues) |
+
+LobsterPy is a package that enables automatic analysis of LOBTSER outputs to get summarized bonding information and relevant bond plots. Additionally, one can also generate features for machine learning studies from LOBSTER outputs.
+
+::::{grid} 1 1 2 2
+:class-container: text-center
+:gutter: 3
+
+
+:::{grid-item-card}
+:link: fundamentals/index
+:link-type: doc
+:class-header: bg-light
+**Fundamental Aspects**
+^^^
+This guide contains a detailed explanation of the key functionalites on 
+which LobsterPy automatic analysis is based on.
+:::
+
+:::{grid-item-card}
+:link: installation/index
+:link-type: doc
+:class-header: bg-light
+**User Guide**
+^^^
+This guide provides in-depth information for getting started and tutorials for *LobsterPy*.
+:::
+
+:::{grid-item-card}
+:link: https://materialsproject.github.io/atomate2/user/codes/vasp.html#lobster
+:class-header: bg-light
+**LOBSTER Workflow**
+^^^
+Here you can find how to use our completely automated workflow to perform bonding analysis with 
+LOBSTER and Lobsterpy via atomate2.
+:::
+
+
+:::{grid-item-card}
+:link: dev/dev_installation
+:link-type: doc
+:class-header: bg-light
+**Developer guide**
+^^^
+Do you want contribute or improve existing functionalities?
+Check out the developer guide.
+:::
+::::
diff --git a/_sources/installation/index.md b/_sources/installation/index.md
@@ -0,0 +1,7 @@
+Getting started
+================
+```{include} ../../README.md
+---
+start-line: 5
+---
+```
diff --git a/_sources/reference/cli.rst b/_sources/reference/cli.rst
@@ -0,0 +1,14 @@
+CLI Reference
+==============
+
+.. toctree::
+   :maxdepth: 1
+
+   cli_subcommands/createinputs
+   cli_subcommands/description
+   cli_subcommands/descriptionquality
+   cli_subcommands/plotauto
+   cli_subcommands/plotautoia
+   cli_subcommands/plotdos
+   cli_subcommands/ploticohpdistance
+   cli_subcommands/plot
diff --git a/_sources/reference/cli_subcommands/createinputs.rst b/_sources/reference/cli_subcommands/createinputs.rst
@@ -0,0 +1,16 @@
+create-inputs
+==============
+
+Create inputs for lobster computation. It works only with PBE POTCARs.
+
+.. hint:: Aliases available
+
+   - createinputs
+
+
+.. argparse::
+   :module: lobsterpy.cli
+   :func: get_parser
+   :prog: lobsterpy
+   :path: create-inputs
+
diff --git a/_sources/reference/cli_subcommands/description.rst b/_sources/reference/cli_subcommands/description.rst
@@ -0,0 +1,11 @@
+description
+============
+
+Deliver a text description of the COHPs or COBIS or COOP results from Lobster and VASP
+
+.. argparse::
+   :module: lobsterpy.cli
+   :func: get_parser
+   :prog: lobsterpy
+   :path: description
+
diff --git a/_sources/reference/cli_subcommands/descriptionquality.rst b/_sources/reference/cli_subcommands/descriptionquality.rst
@@ -0,0 +1,10 @@
+description-quality
+===================
+
+Deliver a text description of the LOBSTER calc quality analysis. Mandatory required files: POSCAR, POTCAR or POTCAR symbols, lobsterout, lobsterin. Optional files (BVA comparison): CHARGE.lobster, (DOS comparison): DOSCAR.lobster/ DOSCAR.LSO.lobster, Vasprun.xml.
+
+.. argparse::
+   :module: lobsterpy.cli
+   :func: get_parser
+   :prog: lobsterpy
+   :path: description-quality
diff --git a/_sources/reference/cli_subcommands/plot.rst b/_sources/reference/cli_subcommands/plot.rst
@@ -0,0 +1,11 @@
+plot
+====
+
+Plot specific COHPs/COBIs/COOPs based on bond numbers.
+
+.. argparse::
+   :module: lobsterpy.cli
+   :func: get_parser
+   :prog: lobsterpy
+   :path: plot
+
diff --git a/_sources/reference/cli_subcommands/plotauto.rst b/_sources/reference/cli_subcommands/plotauto.rst
@@ -0,0 +1,19 @@
+plot-automatic
+==============
+
+Plot most important COHPs or COBIs or COOPs automatically. This option also includes an automatic description.
+
+.. hint:: Aliases available
+
+   - plot-auto
+   - auto-plot
+   - autoplot
+   - automatic-plot
+   - automaticplot
+
+.. argparse::
+   :module: lobsterpy.cli
+   :func: get_parser
+   :prog: lobsterpy
+   :path: plot-automatic
+
diff --git a/_sources/reference/cli_subcommands/plotautoia.rst b/_sources/reference/cli_subcommands/plotautoia.rst
@@ -0,0 +1,18 @@
+plot-automatic-ia
+==================
+
+Creates an interactive plot of most important COHPs or COBIs or COOPs automatically.
+
+.. hint:: Aliases available
+
+   - plot-auto-ia
+   - auto-plot-ia
+   - autoplotia
+   - automatic-plot-ia
+   - automaticplot-ia
+
+.. argparse::
+   :module: lobsterpy.cli
+   :func: get_parser
+   :prog: lobsterpy
+   :path: plot-automatic-ia
diff --git a/_sources/reference/cli_subcommands/plotdos.rst b/_sources/reference/cli_subcommands/plotdos.rst
@@ -0,0 +1,11 @@
+plot-dos
+=========
+
+Plots DOS from lobster computation.
+
+.. argparse::
+   :module: lobsterpy.cli
+   :func: get_parser
+   :prog: lobsterpy
+   :path: plot-dos
+
diff --git a/_sources/reference/cli_subcommands/ploticohpdistance.rst b/_sources/reference/cli_subcommands/ploticohpdistance.rst
@@ -0,0 +1,15 @@
+plot-icohp-distance
+====================
+
+Plot ICOHPs or ICOOPs or ICOBIs with respect to bond lengths.
+
+.. hint:: Aliases available
+
+   - ploticohpdistance
+
+.. argparse::
+   :module: lobsterpy.cli
+   :func: get_parser
+   :prog: lobsterpy
+   :path: plot-icohp-distance
+
diff --git a/_sources/reference/index.rst b/_sources/reference/index.rst
@@ -0,0 +1,15 @@
+Python API reference
+====================
+
+
+.. currentmodule:: lobsterpy
+
+.. autosummary::
+    :recursive:
+    :toctree:
+    :nosignatures:
+
+    cohp
+    featurize
+    plotting
+    structuregraph
diff --git a/_sources/reference/lobsterpy.cohp.analyze.Analysis.rst b/_sources/reference/lobsterpy.cohp.analyze.Analysis.rst
@@ -0,0 +1,8 @@
+Analysis
+========
+
+.. currentmodule:: lobsterpy.cohp.analyze
+
+.. autoclass:: Analysis
+   :show-inheritance:
+   :members:
diff --git a/_sources/reference/lobsterpy.cohp.analyze.rst b/_sources/reference/lobsterpy.cohp.analyze.rst
@@ -0,0 +1,45 @@
+lobsterpy.cohp.analyze
+======================
+
+.. automodule:: lobsterpy.cohp.analyze
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+      :toctree:
+      :nosignatures:
+
+      Analysis
+
+
+
+
+
+
+
+
+
+