move code out of src & fix reference autogeneration accordingly

ryanharvey1 · Oct 7, 2024 · df77deb · df77deb
1 parent 88df175
commit df77deb
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Showing 58 changed files with 7 additions and 3 deletions.
diff --git a/docs/gen_ref_pages.py b/docs/gen_ref_pages.py
@@ -1,17 +1,20 @@
 """Generate the code reference pages."""
+import os
 from itertools import chain
 from pathlib import Path
 
 import mkdocs_gen_files
 
 
 nav = mkdocs_gen_files.Nav()
-mod_symbol = ''#<code class="doc-symbol doc-symbol-nav doc-symbol-module"></code>'
+mod_symbol = '<code class="doc-symbol doc-symbol-nav doc-symbol-module"></code>'
 
 root = Path(__file__).parent.parent
-src = root / 'src'
+src = root
 
-for path in sorted(chain(src.rglob("*.py"), src.rglob("*.pyi"))):
+for path in sorted(src.rglob("*.py")):
+    if path.relative_to(src).parts[0] != "neuro_py":
+        continue
     module_path = path.relative_to(src).with_suffix("")
     doc_path = path.relative_to(src).with_suffix(".md")
     full_doc_path = Path("reference", doc_path)
@@ -26,6 +29,7 @@
         continue
 
     nav_parts = [f"{mod_symbol} {part}" for part in parts]
+    print(nav_parts)
     nav[tuple(nav_parts)[-2:]] = doc_path.as_posix()
 
     with mkdocs_gen_files.open(full_doc_path, "w") as fd:

diff --git a/src/neuro_py/__init__.py → neuro_py/__init__.py b/src/neuro_py/__init__.py → neuro_py/__init__.py
diff --git a/src/neuro_py/__init__.pyi → neuro_py/__init__.pyi b/src/neuro_py/__init__.pyi → neuro_py/__init__.pyi
diff --git a/src/neuro_py/behavior/__init__.py → neuro_py/behavior/__init__.py b/src/neuro_py/behavior/__init__.py → neuro_py/behavior/__init__.py
diff --git a/src/neuro_py/behavior/__init__.pyi → neuro_py/behavior/__init__.pyi b/src/neuro_py/behavior/__init__.pyi → neuro_py/behavior/__init__.pyi
diff --git a/src/neuro_py/behavior/cheeseboard.py → neuro_py/behavior/cheeseboard.py b/src/neuro_py/behavior/cheeseboard.py → neuro_py/behavior/cheeseboard.py
diff --git a/src/neuro_py/behavior/get_trials.py → neuro_py/behavior/get_trials.py b/src/neuro_py/behavior/get_trials.py → neuro_py/behavior/get_trials.py
diff --git a/src/neuro_py/behavior/kinematics.py → neuro_py/behavior/kinematics.py b/src/neuro_py/behavior/kinematics.py → neuro_py/behavior/kinematics.py
diff --git a/src/neuro_py/behavior/linear_positions.py → neuro_py/behavior/linear_positions.py b/src/neuro_py/behavior/linear_positions.py → neuro_py/behavior/linear_positions.py
diff --git a/...uro_py/behavior/linearization_pipeline.py → neuro_py/behavior/linearization_pipeline.py b/...uro_py/behavior/linearization_pipeline.py → neuro_py/behavior/linearization_pipeline.py
diff --git a/...behavior/well_traversal_classification.py → ...behavior/well_traversal_classification.py b/...behavior/well_traversal_classification.py → ...behavior/well_traversal_classification.py
diff --git a/src/neuro_py/ensemble/__init__.py → neuro_py/ensemble/__init__.py b/src/neuro_py/ensemble/__init__.py → neuro_py/ensemble/__init__.py
diff --git a/src/neuro_py/ensemble/__init__.pyi → neuro_py/ensemble/__init__.pyi b/src/neuro_py/ensemble/__init__.pyi → neuro_py/ensemble/__init__.pyi
diff --git a/src/neuro_py/ensemble/assembly.py → neuro_py/ensemble/assembly.py b/src/neuro_py/ensemble/assembly.py → neuro_py/ensemble/assembly.py
diff --git a/...euro_py/ensemble/assembly_reactivation.py → neuro_py/ensemble/assembly_reactivation.py b/...euro_py/ensemble/assembly_reactivation.py → neuro_py/ensemble/assembly_reactivation.py
diff --git a/src/neuro_py/ensemble/explained_variance.py → neuro_py/ensemble/explained_variance.py b/src/neuro_py/ensemble/explained_variance.py → neuro_py/ensemble/explained_variance.py
diff --git a/src/neuro_py/ensemble/replay.py → neuro_py/ensemble/replay.py b/src/neuro_py/ensemble/replay.py → neuro_py/ensemble/replay.py
diff --git a/src/neuro_py/ensemble/similarity_index.py → neuro_py/ensemble/similarity_index.py b/src/neuro_py/ensemble/similarity_index.py → neuro_py/ensemble/similarity_index.py
diff --git a/src/neuro_py/ensemble/similaritymat.py → neuro_py/ensemble/similaritymat.py b/src/neuro_py/ensemble/similaritymat.py → neuro_py/ensemble/similaritymat.py
diff --git a/src/neuro_py/io/__init__.py → neuro_py/io/__init__.py b/src/neuro_py/io/__init__.py → neuro_py/io/__init__.py
diff --git a/src/neuro_py/io/__init__.pyi → neuro_py/io/__init__.pyi b/src/neuro_py/io/__init__.pyi → neuro_py/io/__init__.pyi
diff --git a/src/neuro_py/io/loading.py → neuro_py/io/loading.py b/src/neuro_py/io/loading.py → neuro_py/io/loading.py
diff --git a/src/neuro_py/io/saving.py → neuro_py/io/saving.py b/src/neuro_py/io/saving.py → neuro_py/io/saving.py
diff --git a/src/neuro_py/lfp/CSD.py → neuro_py/lfp/CSD.py b/src/neuro_py/lfp/CSD.py → neuro_py/lfp/CSD.py
diff --git a/src/neuro_py/lfp/__init__.py → neuro_py/lfp/__init__.py b/src/neuro_py/lfp/__init__.py → neuro_py/lfp/__init__.py
diff --git a/src/neuro_py/lfp/__init__.pyi → neuro_py/lfp/__init__.pyi b/src/neuro_py/lfp/__init__.pyi → neuro_py/lfp/__init__.pyi
diff --git a/src/neuro_py/lfp/preprocessing.py → neuro_py/lfp/preprocessing.py b/src/neuro_py/lfp/preprocessing.py → neuro_py/lfp/preprocessing.py
diff --git a/src/neuro_py/lfp/spectral.py → neuro_py/lfp/spectral.py b/src/neuro_py/lfp/spectral.py → neuro_py/lfp/spectral.py
diff --git a/src/neuro_py/lfp/theta_cycles.py → neuro_py/lfp/theta_cycles.py b/src/neuro_py/lfp/theta_cycles.py → neuro_py/lfp/theta_cycles.py
diff --git a/src/neuro_py/plotting/__init__.py → neuro_py/plotting/__init__.py b/src/neuro_py/plotting/__init__.py → neuro_py/plotting/__init__.py
diff --git a/src/neuro_py/plotting/__init__.pyi → neuro_py/plotting/__init__.pyi b/src/neuro_py/plotting/__init__.pyi → neuro_py/plotting/__init__.pyi
diff --git a/src/neuro_py/plotting/events.py → neuro_py/plotting/events.py b/src/neuro_py/plotting/events.py → neuro_py/plotting/events.py
diff --git a/src/neuro_py/plotting/figure_helpers.py → neuro_py/plotting/figure_helpers.py b/src/neuro_py/plotting/figure_helpers.py → neuro_py/plotting/figure_helpers.py
diff --git a/src/neuro_py/process/__init__.py → neuro_py/process/__init__.py b/src/neuro_py/process/__init__.py → neuro_py/process/__init__.py
diff --git a/src/neuro_py/process/__init__.pyi → neuro_py/process/__init__.pyi b/src/neuro_py/process/__init__.pyi → neuro_py/process/__init__.pyi
diff --git a/src/neuro_py/process/batch_analysis.py → neuro_py/process/batch_analysis.py b/src/neuro_py/process/batch_analysis.py → neuro_py/process/batch_analysis.py
diff --git a/src/neuro_py/process/correlations.py → neuro_py/process/correlations.py b/src/neuro_py/process/correlations.py → neuro_py/process/correlations.py
diff --git a/src/neuro_py/process/intervals.py → neuro_py/process/intervals.py b/src/neuro_py/process/intervals.py → neuro_py/process/intervals.py
diff --git a/src/neuro_py/process/peri_event.py → neuro_py/process/peri_event.py b/src/neuro_py/process/peri_event.py → neuro_py/process/peri_event.py
diff --git a/src/neuro_py/process/precession_utils.py → neuro_py/process/precession_utils.py b/src/neuro_py/process/precession_utils.py → neuro_py/process/precession_utils.py
diff --git a/src/neuro_py/process/pychronux.py → neuro_py/process/pychronux.py b/src/neuro_py/process/pychronux.py → neuro_py/process/pychronux.py
diff --git a/src/neuro_py/process/utils.py → neuro_py/process/utils.py b/src/neuro_py/process/utils.py → neuro_py/process/utils.py
diff --git a/src/neuro_py/session/__init__.py → neuro_py/session/__init__.py b/src/neuro_py/session/__init__.py → neuro_py/session/__init__.py
diff --git a/src/neuro_py/session/__init__.pyi → neuro_py/session/__init__.pyi b/src/neuro_py/session/__init__.pyi → neuro_py/session/__init__.pyi
diff --git a/src/neuro_py/session/locate_epochs.py → neuro_py/session/locate_epochs.py b/src/neuro_py/session/locate_epochs.py → neuro_py/session/locate_epochs.py
diff --git a/src/neuro_py/spikes/__init__.py → neuro_py/spikes/__init__.py b/src/neuro_py/spikes/__init__.py → neuro_py/spikes/__init__.py
diff --git a/src/neuro_py/spikes/__init__.pyi → neuro_py/spikes/__init__.pyi b/src/neuro_py/spikes/__init__.pyi → neuro_py/spikes/__init__.pyi
diff --git a/src/neuro_py/spikes/spike_tools.py → neuro_py/spikes/spike_tools.py b/src/neuro_py/spikes/spike_tools.py → neuro_py/spikes/spike_tools.py
diff --git a/src/neuro_py/stats/__init__.py → neuro_py/stats/__init__.py b/src/neuro_py/stats/__init__.py → neuro_py/stats/__init__.py
diff --git a/src/neuro_py/stats/__init__.pyi → neuro_py/stats/__init__.pyi b/src/neuro_py/stats/__init__.pyi → neuro_py/stats/__init__.pyi
diff --git a/src/neuro_py/stats/circ_stats.py → neuro_py/stats/circ_stats.py b/src/neuro_py/stats/circ_stats.py → neuro_py/stats/circ_stats.py
diff --git a/src/neuro_py/stats/regression.py → neuro_py/stats/regression.py b/src/neuro_py/stats/regression.py → neuro_py/stats/regression.py
diff --git a/src/neuro_py/stats/stats.py → neuro_py/stats/stats.py b/src/neuro_py/stats/stats.py → neuro_py/stats/stats.py
diff --git a/src/neuro_py/stats/system_identifier.py → neuro_py/stats/system_identifier.py b/src/neuro_py/stats/system_identifier.py → neuro_py/stats/system_identifier.py
diff --git a/src/neuro_py/tuning/__init__.py → neuro_py/tuning/__init__.py b/src/neuro_py/tuning/__init__.py → neuro_py/tuning/__init__.py
diff --git a/src/neuro_py/tuning/__init__.pyi → neuro_py/tuning/__init__.pyi b/src/neuro_py/tuning/__init__.pyi → neuro_py/tuning/__init__.pyi
diff --git a/src/neuro_py/tuning/fields.py → neuro_py/tuning/fields.py b/src/neuro_py/tuning/fields.py → neuro_py/tuning/fields.py
diff --git a/src/neuro_py/tuning/maps.py → neuro_py/tuning/maps.py b/src/neuro_py/tuning/maps.py → neuro_py/tuning/maps.py