Cleanup notebooks and docs

Add .readthedocs.yaml
tiqi-group · Nov 7, 2024 · 787fd3e · 787fd3e
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diff --git a/.gitignore b/.gitignore
@@ -1,5 +1,6 @@
 *.cache
-notebooks/_ignored/
+.vscode
+.python-version
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,20 @@
+# Read the Docs configuration file for MkDocs projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+# Poetry setup: https://github.com/readthedocs/readthedocs.org/issues/4912#issuecomment-1992286540
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+  jobs:
+    post_create_environment:
+      - python -m pip install poetry
+    post_install:
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs
+
+mkdocs:
+  configuration: mkdocs.yaml
diff --git a/.vscode/settings.json b/.vscode/settings.json
diff --git a/AUTHORS b/AUTHORS
diff --git a/CHANGES → CHANGELOG b/CHANGES → CHANGELOG
@@ -17,4 +17,4 @@
 - Fix bug in wigner_6j cache
 
 0.0.2 (2021-10-13)
-------------------
+------------------
diff --git a/README.md b/README.md
diff --git a/notebooks/TODO.md → _notebooks/TODO.md b/notebooks/TODO.md → _notebooks/TODO.md
diff --git a/notebooks/atom_from_database.ipynb → _notebooks/atom_from_database.ipynb b/notebooks/atom_from_database.ipynb → _notebooks/atom_from_database.ipynb
diff --git a/notebooks/atom_transition_graph.ipynb → _notebooks/atom_transition_graph.ipynb b/notebooks/atom_transition_graph.ipynb → _notebooks/atom_transition_graph.ipynb
diff --git a/notebooks/atomphys_plot.ipynb → _notebooks/atomphys_plot.ipynb b/notebooks/atomphys_plot.ipynb → _notebooks/atomphys_plot.ipynb
diff --git a/notebooks/matrix_element.ipynb → _notebooks/matrix_element.ipynb b/notebooks/matrix_element.ipynb → _notebooks/matrix_element.ipynb
diff --git a/notebooks/test_hamiltonians.ipynb → _notebooks/test_hamiltonians.ipynb b/notebooks/test_hamiltonians.ipynb → _notebooks/test_hamiltonians.ipynb
diff --git a/notebooks/understand_atomphys.ipynb → _notebooks/understand_atomphys.ipynb b/notebooks/understand_atomphys.ipynb → _notebooks/understand_atomphys.ipynb
diff --git a/notebooks/zeeman_and_hyperfine.ipynb → _notebooks/zeeman_and_hyperfine.ipynb b/notebooks/zeeman_and_hyperfine.ipynb → _notebooks/zeeman_and_hyperfine.ipynb
diff --git a/_trash/_old_README.md b/_trash/_old_README.md
diff --git a/_tests/__init__.py → _trash/_tests/__init__.py b/_tests/__init__.py → _trash/_tests/__init__.py
diff --git a/_tests/conftest.py → _trash/_tests/conftest.py b/_tests/conftest.py → _trash/_tests/conftest.py
diff --git a/_tests/test_ASD_import.py → _trash/_tests/test_ASD_import.py b/_tests/test_ASD_import.py → _trash/_tests/test_ASD_import.py
diff --git a/_tests/test_Rb.py → _trash/_tests/test_Rb.py b/_tests/test_Rb.py → _trash/_tests/test_Rb.py
diff --git a/_tests/test_atom.py → _trash/_tests/test_atom.py b/_tests/test_atom.py → _trash/_tests/test_atom.py
diff --git a/_tests/test_laser.py → _trash/_tests/test_laser.py b/_tests/test_laser.py → _trash/_tests/test_laser.py
diff --git a/_tests/test_nist.py → _trash/_tests/test_nist.py b/_tests/test_nist.py → _trash/_tests/test_nist.py
diff --git a/_tests/test_polarizability.py → _trash/_tests/test_polarizability.py b/_tests/test_polarizability.py → _trash/_tests/test_polarizability.py
diff --git a/_tests/test_state.py → _trash/_tests/test_state.py b/_tests/test_state.py → _trash/_tests/test_state.py
diff --git a/_tests/test_term.py → _trash/_tests/test_term.py b/_tests/test_term.py → _trash/_tests/test_term.py
diff --git a/_tests/test_transition.py → _trash/_tests/test_transition.py b/_tests/test_transition.py → _trash/_tests/test_transition.py
diff --git a/_tests/test_util.py → _trash/_tests/test_util.py b/_tests/test_util.py → _trash/_tests/test_util.py
diff --git a/_tests/test_wigner.py → _trash/_tests/test_wigner.py b/_tests/test_wigner.py → _trash/_tests/test_wigner.py
diff --git a/docs/CNAME b/docs/CNAME
diff --git a/data.md → docs/data.md b/data.md → docs/data.md
diff --git a/docs/developers.md b/docs/developers.md
diff --git a/docs/index.md b/docs/index.md
@@ -1,13 +1 @@
-This document provides a guide to the Python module designed for atomic physics calculations. The idea behind this module is to explore atomic physics, properties of atoms, and understand their electron dynamics in light fields. 
-
-The package should be primarily used for bosonic isotopes, where the hyperfine structure is not present. We decided to initially release the package with simplified structure such that to get a feeling for the usefullness of the tool to the community. In case of interest, we can extend this package to include calculations for the fermionic isotopes.
-
-I hope this will be helpfull for many.
-
-The documentation is divided into three subsections, which each discuss different potential use-cases of atomphys:
-
-1. **Core** - Here we discuss how atomphys can be used as python API for NIST database and other databases
-2. **Calculations** - Here we discuss the theory behind the calculations with which atomphys can help
-3. **Helper functions for qutip** - Here we discuss how atomphys can be usef to build light-atom hamiltonians that can be directly parsed to qutip and can be solved
-
-
+{% include-markdown "../README.md" %}
diff --git a/mkdocs.yml → mkdocs.yaml b/mkdocs.yml → mkdocs.yaml
@@ -1,7 +1,7 @@
 site_name: atomphys
-site_url: https://mgrau.github.io/atomphys
-repo_url: https://github.com/mgrau/atomphys
-edit_uri: edit/main/docs/
+site_url: https://atomphys.readthedocs.io
+repo_url: https://github.com/tiqi-group/atomphys
+edit_uri: blob/docs/docs/
 repo_name: atomphys
 use_directory_urls: false
 
@@ -16,12 +16,12 @@ nav:
         - Matrix Elements: user_guide/calculations/matrix_elements.md
         - Rabi Frequencies: user_guide/calculations/rabi_frequencies.md
         - AC Stark Shifts: user_guide/calculations/ac_stark_shifts.md
-        - Linewidhts: user_guide/calculations/linewidths.md
+        - Linewidths: user_guide/calculations/linewidths.md
       - Qutip Helpers:
         - Master Equation: user_guide/qutip_helpers/master_equation.md
         - Hamiltonians: user_guide/qutip_helpers/hamiltonians.md
         - Collapse Operators: user_guide/qutip_helpers/collapse_operators.md
-  - Developers: developers.md
+  - Data References: data.md
 
 theme:
   logo: img/atom.svg
@@ -69,12 +69,14 @@ extra_css:
 plugins:
   - search
   - include-markdown
+  - mkdocstrings:
+      default_handler: python
+      handlers:
+        python:
+          paths: [atomphys] # search packages in the src folder
   # - mknotebooks:
   #     execute: true
   #     enable_default_jupyter_cell_styling: false
   #     binder: true
   #     binder_service_name: "gh/mgrau"
   #     binder_branch: "main"
-  # - mkdocstrings:
-  #     watch:
-  #       - atomphys