From e61805120fa14a0de8fc9157b1bc1a5ef559051d Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Thu, 8 Sep 2022 15:06:36 +0200 Subject: [PATCH 01/25] re-enable tools on the API documentation --- docs/api/interfaces.icephys.rst | 2 +- docs/api/tools.rst | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/docs/api/interfaces.icephys.rst b/docs/api/interfaces.icephys.rst index 1c0a7be86..57386ccdb 100644 --- a/docs/api/interfaces.icephys.rst +++ b/docs/api/interfaces.icephys.rst @@ -1,5 +1,5 @@ Intracellular electrophysiology -=================== +=============================== Base Interface -------------- diff --git a/docs/api/tools.rst b/docs/api/tools.rst index d5caa212a..6cbeb85f7 100644 --- a/docs/api/tools.rst +++ b/docs/api/tools.rst @@ -1,6 +1,10 @@ Tools ===== +.. automodule:: neuroconv + :members: + :no-undoc-members: + .. toctree:: :maxdepth: 4 From 3cac88c453327ec1431496e1e367d08ffd2ed732 Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Thu, 8 Sep 2022 15:24:10 +0200 Subject: [PATCH 02/25] add missing modules, neo and roi iterator --- docs/api/interfaces.icephys.rst | 2 +- docs/api/tools.neo.rst | 4 ++++ docs/api/tools.roiextractors.rst | 7 +++++++ docs/api/tools.rst | 1 + 4 files changed, 13 insertions(+), 1 deletion(-) create mode 100644 docs/api/tools.neo.rst diff --git a/docs/api/interfaces.icephys.rst b/docs/api/interfaces.icephys.rst index 57386ccdb..7ca3e6aa7 100644 --- a/docs/api/interfaces.icephys.rst +++ b/docs/api/interfaces.icephys.rst @@ -7,5 +7,5 @@ Base Interface Abf Interface -------------------- +------------- .. automodule:: neuroconv.datainterfaces.icephys.abf.abfdatainterface diff --git a/docs/api/tools.neo.rst b/docs/api/tools.neo.rst new file mode 100644 index 000000000..3c482467a --- /dev/null +++ b/docs/api/tools.neo.rst @@ -0,0 +1,4 @@ +NEO +--- + +.. automodule:: neuroconv.tools.neo.neo diff --git a/docs/api/tools.roiextractors.rst b/docs/api/tools.roiextractors.rst index c585eab72..f84e9cc6f 100644 --- a/docs/api/tools.roiextractors.rst +++ b/docs/api/tools.roiextractors.rst @@ -1,3 +1,10 @@ ROI extractors ============== + +Interface with roiextractors +---------------------------- .. automodule:: neuroconv.tools.roiextractors.roiextractors + +Imaging exctractor iterator +-------------------------- +.. automodule:: neuroconv.tools.roiextractors.imagingextractordatachunkiterator diff --git a/docs/api/tools.rst b/docs/api/tools.rst index 6cbeb85f7..c9e61e69a 100644 --- a/docs/api/tools.rst +++ b/docs/api/tools.rst @@ -11,3 +11,4 @@ Tools tools.spikeinterface tools.roiextractors tools.yaml_to_nwb_conversion + tools.neo From 42a413c1f5e76c972dde17c380a189cad454ab4f Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Thu, 8 Sep 2022 15:31:15 +0200 Subject: [PATCH 03/25] update configuration --- .readthedocs.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 11662e251..60ea831e7 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -6,9 +6,9 @@ version: 2 # Set the version of Python and other tools you might need build: - os: ubuntu-20.04 + os: ubuntu-22.04 tools: - python: "3.8" + python: "3.9" # Build documentation in the docs/ directory with Sphinx sphinx: From 96db2198961cb504a525610bfdf4753ff5790862 Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Thu, 8 Sep 2022 15:52:09 +0200 Subject: [PATCH 04/25] try explicit links --- docs/api/tools.roiextractors.rst | 4 +--- docs/api/tools.rst | 4 ++-- docs/api/tools.spikeinterface.rst | 3 --- docs/conversion_examples_gallery/sorting/blackrock.rst | 1 + 4 files changed, 4 insertions(+), 8 deletions(-) diff --git a/docs/api/tools.roiextractors.rst b/docs/api/tools.roiextractors.rst index f84e9cc6f..14f965e7e 100644 --- a/docs/api/tools.roiextractors.rst +++ b/docs/api/tools.roiextractors.rst @@ -1,10 +1,8 @@ -ROI extractors -============== Interface with roiextractors ---------------------------- .. automodule:: neuroconv.tools.roiextractors.roiextractors Imaging exctractor iterator --------------------------- +--------------------------- .. automodule:: neuroconv.tools.roiextractors.imagingextractordatachunkiterator diff --git a/docs/api/tools.rst b/docs/api/tools.rst index c9e61e69a..76428a34d 100644 --- a/docs/api/tools.rst +++ b/docs/api/tools.rst @@ -8,7 +8,7 @@ Tools .. toctree:: :maxdepth: 4 - tools.spikeinterface - tools.roiextractors + Spike Interface + ROI extractors tools.yaml_to_nwb_conversion tools.neo diff --git a/docs/api/tools.spikeinterface.rst b/docs/api/tools.spikeinterface.rst index a0e18357b..cfa1543b9 100644 --- a/docs/api/tools.spikeinterface.rst +++ b/docs/api/tools.spikeinterface.rst @@ -1,6 +1,3 @@ -Spike Interface -=============== - Interface with spikeinterface ----------------------------- .. automodule:: neuroconv.tools.spikeinterface.spikeinterface diff --git a/docs/conversion_examples_gallery/sorting/blackrock.rst b/docs/conversion_examples_gallery/sorting/blackrock.rst index 0bfa8c8bb..9cf917d24 100644 --- a/docs/conversion_examples_gallery/sorting/blackrock.rst +++ b/docs/conversion_examples_gallery/sorting/blackrock.rst @@ -9,6 +9,7 @@ Install NeuroConv with the additional dependencies necessary for reading Blackro Convert Blackrock sorting data to NWB using :py:class:`~neuroconv.datainterfaces.ecephys.blackrock.blackrockdatainterface.BlackrockSortingInterface`. .. code-block:: python + >>> from datetime import datetime >>> from dateutil import tz >>> from pathlib import Path From 63449ebea7b770b7153addcf037321dba7cc0589 Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Thu, 8 Sep 2022 16:26:58 +0200 Subject: [PATCH 05/25] test to see builds --- docs/api/interfaces.rst | 4 ---- docs/api/tools.roiextractors.rst | 3 +++ docs/api/tools.rst | 4 ---- docs/api/tools.spikeinterface.rst | 3 +++ 4 files changed, 6 insertions(+), 8 deletions(-) diff --git a/docs/api/interfaces.rst b/docs/api/interfaces.rst index 809a2c7d4..c46a25588 100644 --- a/docs/api/interfaces.rst +++ b/docs/api/interfaces.rst @@ -1,10 +1,6 @@ Interfaces ============ -.. automodule:: neuroconv - :members: - :no-undoc-members: - .. toctree:: :maxdepth: 4 diff --git a/docs/api/tools.roiextractors.rst b/docs/api/tools.roiextractors.rst index 14f965e7e..cb807b43a 100644 --- a/docs/api/tools.roiextractors.rst +++ b/docs/api/tools.roiextractors.rst @@ -1,4 +1,7 @@ +ROI extractors +============== + Interface with roiextractors ---------------------------- .. automodule:: neuroconv.tools.roiextractors.roiextractors diff --git a/docs/api/tools.rst b/docs/api/tools.rst index 76428a34d..296386d85 100644 --- a/docs/api/tools.rst +++ b/docs/api/tools.rst @@ -1,10 +1,6 @@ Tools ===== -.. automodule:: neuroconv - :members: - :no-undoc-members: - .. toctree:: :maxdepth: 4 diff --git a/docs/api/tools.spikeinterface.rst b/docs/api/tools.spikeinterface.rst index cfa1543b9..a0e18357b 100644 --- a/docs/api/tools.spikeinterface.rst +++ b/docs/api/tools.spikeinterface.rst @@ -1,3 +1,6 @@ +Spike Interface +=============== + Interface with spikeinterface ----------------------------- .. automodule:: neuroconv.tools.spikeinterface.spikeinterface From 9ccbf41e984930102de4279b260f7dc38756618b Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Thu, 8 Sep 2022 17:22:29 +0200 Subject: [PATCH 06/25] test II --- docs/api/tools.roiextractors.rst | 5 +++-- docs/api/tools.rst | 2 +- docs/conf.py | 6 +++--- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/docs/api/tools.roiextractors.rst b/docs/api/tools.roiextractors.rst index cb807b43a..f1e884b84 100644 --- a/docs/api/tools.roiextractors.rst +++ b/docs/api/tools.roiextractors.rst @@ -6,6 +6,7 @@ Interface with roiextractors ---------------------------- .. automodule:: neuroconv.tools.roiextractors.roiextractors -Imaging exctractor iterator ---------------------------- + +Imaging extractor iterator +-------------------------- .. automodule:: neuroconv.tools.roiextractors.imagingextractordatachunkiterator diff --git a/docs/api/tools.rst b/docs/api/tools.rst index 296386d85..3ff527892 100644 --- a/docs/api/tools.rst +++ b/docs/api/tools.rst @@ -5,6 +5,6 @@ Tools :maxdepth: 4 Spike Interface - ROI extractors + tools.roiextractors tools.yaml_to_nwb_conversion tools.neo diff --git a/docs/conf.py b/docs/conf.py index 85069b43b..1ccaa6a65 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -50,9 +50,9 @@ napoleon_include_special_with_doc = True # Autodoc -autoclass_content = "both" -autodoc_member_order = "bysource" -autodata_content = "both" +autoclass_content = "both" # Concatenates docstring of the class with that of its __init__ +autodoc_member_order = "bysource" # Displays classes and methods by their order in source code +autodata_content = "both" # autodoc_default_options = { "members": True, "member-order": "bysource", From 3fc54530f67c4d17314de7b6a858f8a297b5e382 Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Fri, 23 Sep 2022 18:30:19 +0200 Subject: [PATCH 07/25] testing import problem --- docs/conf.py | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/conf.py b/docs/conf.py index fb8ecafb0..17bd45c9f 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -3,6 +3,7 @@ from pathlib import Path sys.path.insert(0, str(Path(__file__).resolve().parents[1])) +from neuroconv.tools import spikeinterface project = "NeuroConv" copyright = "2022, CatalystNeuro" From 8239b9525a33626aa68b729a2d187d8987934dce Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Fri, 23 Sep 2022 18:38:27 +0200 Subject: [PATCH 08/25] installing everything in docs --- docs/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index 17bd45c9f..04efea262 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -3,7 +3,7 @@ from pathlib import Path sys.path.insert(0, str(Path(__file__).resolve().parents[1])) -from neuroconv.tools import spikeinterface +# from neuroconv.tools import spikeinterface project = "NeuroConv" copyright = "2022, CatalystNeuro" From cc1fe81e4c9d1f9d9573e85f4af48b0fe606ee2c Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Fri, 23 Sep 2022 18:41:22 +0200 Subject: [PATCH 09/25] test import again --- docs/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index 04efea262..17bd45c9f 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -3,7 +3,7 @@ from pathlib import Path sys.path.insert(0, str(Path(__file__).resolve().parents[1])) -# from neuroconv.tools import spikeinterface +from neuroconv.tools import spikeinterface project = "NeuroConv" copyright = "2022, CatalystNeuro" From a8629046fb3f4ad62104200d7790874767597417 Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Fri, 23 Sep 2022 18:47:25 +0200 Subject: [PATCH 10/25] import test --- .readthedocs.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 60ea831e7..4580927b3 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -21,4 +21,5 @@ python: - method: pip path: . extra_requirements: + - full - docs From edf54be63aa6780a3d802894c240b14b1e74ebf5 Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Fri, 23 Sep 2022 18:54:32 +0200 Subject: [PATCH 11/25] test no import in conf file --- docs/conf.py | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index 17bd45c9f..fb8ecafb0 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -3,7 +3,6 @@ from pathlib import Path sys.path.insert(0, str(Path(__file__).resolve().parents[1])) -from neuroconv.tools import spikeinterface project = "NeuroConv" copyright = "2022, CatalystNeuro" From eea96d9fd7d0905d1eae1e938315d7289b250dd2 Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Fri, 23 Sep 2022 19:29:45 +0200 Subject: [PATCH 12/25] fine tunning testing dependencies --- docs/conf.py | 4 ++-- requirements-rtd.txt | 1 + 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index fb8ecafb0..977bb5402 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -53,7 +53,7 @@ # Autodoc autoclass_content = "both" # Concatenates docstring of the class with that of its __init__ autodoc_member_order = "bysource" # Displays classes and methods by their order in source code -autodata_content = "both" # +autodata_content = "both" autodoc_default_options = { "members": True, "member-order": "bysource", @@ -70,7 +70,7 @@ def _correct_signatures(app, what, name, obj, options, signature, return_annotat return (signature, return_annotation) -def setup(app): +def setup(app): # This makes the data-interfaces display, they don't otherwise app.connect("autodoc-process-signature", _correct_signatures) diff --git a/requirements-rtd.txt b/requirements-rtd.txt index 81e08ed2e..fc4216a5f 100644 --- a/requirements-rtd.txt +++ b/requirements-rtd.txt @@ -5,3 +5,4 @@ sphinx_rtd_theme==1.0.0 readthedocs-sphinx-search==0.1.2 sphinx-toggleprompt==0.2.0 sphinx-copybutton==0.5.0 +spikeinterface>=0.95.1 # Necessary to display tools.spikeinterface From de15fd72409b085747a43ce21eb8ac609dc4e70c Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Fri, 23 Sep 2022 19:40:28 +0200 Subject: [PATCH 13/25] test roiextractors display --- .readthedocs.yaml | 1 - docs/conf.py | 10 ++++------ requirements-rtd.txt | 1 + 3 files changed, 5 insertions(+), 7 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 4580927b3..60ea831e7 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -21,5 +21,4 @@ python: - method: pip path: . extra_requirements: - - full - docs diff --git a/docs/conf.py b/docs/conf.py index 977bb5402..dd434495d 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -11,9 +11,9 @@ extensions = [ "sphinx.ext.napoleon", # Support for NumPy and Google style docstrings "sphinx.ext.autodoc", # Includes documentation from docstrings in docs/api - "sphinx.ext.autosummary", # To-add + "sphinx.ext.autosummary", # Not clear. Please add if you know "sphinx_toggleprompt", # Used to control >>> behavior in the conversion gallery example doctests - "sphinx_copybutton", # Used to control the copy button behavior in the conversion gallery doctsts + "sphinx_copybutton", # Used to control the copy button behavior in the conversion gallery doctests "sphinx.ext.intersphinx", # Allows links to other sphinx project documentation sites "sphinx_search.extension", # Allows for auto search function the documentation "sphinx.ext.viewcode", # Shows source code in the documentation @@ -26,13 +26,11 @@ html_theme = "sphinx_rtd_theme" html_static_path = ["_static"] -# These paths are either relative to html_static_path -# or fully qualified paths (eg. https://...) +# These paths are either relative to html_static_path or fully qualified paths (eg. https://...) html_css_files = [ "css/custom.css", ] - html_theme_options = { "collapse_navigation": False, } @@ -70,7 +68,7 @@ def _correct_signatures(app, what, name, obj, options, signature, return_annotat return (signature, return_annotation) -def setup(app): # This makes the data-interfaces display, they don't otherwise +def setup(app): # This makes the data-interfaces signatures display on the docs/api, they don't otherwise app.connect("autodoc-process-signature", _correct_signatures) diff --git a/requirements-rtd.txt b/requirements-rtd.txt index fc4216a5f..0e62498f2 100644 --- a/requirements-rtd.txt +++ b/requirements-rtd.txt @@ -6,3 +6,4 @@ readthedocs-sphinx-search==0.1.2 sphinx-toggleprompt==0.2.0 sphinx-copybutton==0.5.0 spikeinterface>=0.95.1 # Necessary to display tools.spikeinterface +roiextractors>=0.5.0 # Necessary to displays tools.roiextractors From 5d843b71c91528d6ee486541699bac1953bfb573 Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Fri, 23 Sep 2022 19:46:12 +0200 Subject: [PATCH 14/25] test import again --- docs/conf.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/conf.py b/docs/conf.py index dd434495d..b2183325f 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -3,6 +3,8 @@ from pathlib import Path sys.path.insert(0, str(Path(__file__).resolve().parents[1])) +from neuroconv.tools import spikeinterface +from neuroconv.tools import roiextractors project = "NeuroConv" copyright = "2022, CatalystNeuro" From 75454f065ed67e06c1239cb8fa62e7deb0546a6e Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Fri, 23 Sep 2022 19:48:47 +0200 Subject: [PATCH 15/25] testing import twice --- requirements-rtd.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements-rtd.txt b/requirements-rtd.txt index 0e62498f2..5cce1a405 100644 --- a/requirements-rtd.txt +++ b/requirements-rtd.txt @@ -6,4 +6,5 @@ readthedocs-sphinx-search==0.1.2 sphinx-toggleprompt==0.2.0 sphinx-copybutton==0.5.0 spikeinterface>=0.95.1 # Necessary to display tools.spikeinterface +spikeextractors>=0.9.10 # Necessary to display tools.spikeinterface roiextractors>=0.5.0 # Necessary to displays tools.roiextractors From 749118080f825962c0c7cabfa68b0fae2bf4fcaa Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Fri, 23 Sep 2022 19:54:21 +0200 Subject: [PATCH 16/25] try specific modalities --- .readthedocs.yaml | 2 ++ requirements-rtd.txt | 3 --- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 60ea831e7..3bf448e7a 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -22,3 +22,5 @@ python: path: . extra_requirements: - docs + - ecephys + - ophys diff --git a/requirements-rtd.txt b/requirements-rtd.txt index 5cce1a405..81e08ed2e 100644 --- a/requirements-rtd.txt +++ b/requirements-rtd.txt @@ -5,6 +5,3 @@ sphinx_rtd_theme==1.0.0 readthedocs-sphinx-search==0.1.2 sphinx-toggleprompt==0.2.0 sphinx-copybutton==0.5.0 -spikeinterface>=0.95.1 # Necessary to display tools.spikeinterface -spikeextractors>=0.9.10 # Necessary to display tools.spikeinterface -roiextractors>=0.5.0 # Necessary to displays tools.roiextractors From 6aa3935bf7ecf18ac62e5504b220cc496c44e730 Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Fri, 23 Sep 2022 20:02:15 +0200 Subject: [PATCH 17/25] change conf --- docs/conf.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index b2183325f..dd434495d 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -3,8 +3,6 @@ from pathlib import Path sys.path.insert(0, str(Path(__file__).resolve().parents[1])) -from neuroconv.tools import spikeinterface -from neuroconv.tools import roiextractors project = "NeuroConv" copyright = "2022, CatalystNeuro" From 0a9ee1a614853f34fefe1455ceade4adcd31f275 Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Fri, 23 Sep 2022 20:05:38 +0200 Subject: [PATCH 18/25] try full again --- .readthedocs.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 3bf448e7a..8c8b525d3 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -22,5 +22,4 @@ python: path: . extra_requirements: - docs - - ecephys - - ophys + - full From 57778970081224c0f0e6d747bb4b8435fec5a886 Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Fri, 23 Sep 2022 20:11:08 +0200 Subject: [PATCH 19/25] try spikeitnerface again with only spikeinterface --- .readthedocs.yaml | 1 - docs/conf.py | 1 + requirements-rtd.txt | 3 +++ 3 files changed, 4 insertions(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 8c8b525d3..60ea831e7 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -22,4 +22,3 @@ python: path: . extra_requirements: - docs - - full diff --git a/docs/conf.py b/docs/conf.py index dd434495d..0e8efd530 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -3,6 +3,7 @@ from pathlib import Path sys.path.insert(0, str(Path(__file__).resolve().parents[1])) +import neuroconv.tools.roiextractors.roiextractors project = "NeuroConv" copyright = "2022, CatalystNeuro" diff --git a/requirements-rtd.txt b/requirements-rtd.txt index 81e08ed2e..5cce1a405 100644 --- a/requirements-rtd.txt +++ b/requirements-rtd.txt @@ -5,3 +5,6 @@ sphinx_rtd_theme==1.0.0 readthedocs-sphinx-search==0.1.2 sphinx-toggleprompt==0.2.0 sphinx-copybutton==0.5.0 +spikeinterface>=0.95.1 # Necessary to display tools.spikeinterface +spikeextractors>=0.9.10 # Necessary to display tools.spikeinterface +roiextractors>=0.5.0 # Necessary to displays tools.roiextractors From 1a40b1760427813cc7cc3307708add62b9e067b2 Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Fri, 23 Sep 2022 20:18:19 +0200 Subject: [PATCH 20/25] test import imaging --- docs/api/tools.roiextractors.rst | 1 - docs/conf.py | 2 +- src/neuroconv/tools/roiextractors/roiextractors.py | 1 + 3 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/api/tools.roiextractors.rst b/docs/api/tools.roiextractors.rst index f1e884b84..02f3a0a83 100644 --- a/docs/api/tools.roiextractors.rst +++ b/docs/api/tools.roiextractors.rst @@ -1,4 +1,3 @@ - ROI extractors ============== diff --git a/docs/conf.py b/docs/conf.py index 0e8efd530..2b6a5dcd7 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -3,7 +3,7 @@ from pathlib import Path sys.path.insert(0, str(Path(__file__).resolve().parents[1])) -import neuroconv.tools.roiextractors.roiextractors +from neuroconv.tools.roiextractors.imagingextractordatachunkiterator import GenericDataChunkIterator project = "NeuroConv" copyright = "2022, CatalystNeuro" diff --git a/src/neuroconv/tools/roiextractors/roiextractors.py b/src/neuroconv/tools/roiextractors/roiextractors.py index 7631ef147..3a9cd2eb3 100644 --- a/src/neuroconv/tools/roiextractors/roiextractors.py +++ b/src/neuroconv/tools/roiextractors/roiextractors.py @@ -169,6 +169,7 @@ def add_devices(nwbfile: NWBFile, metadata: dict) -> NWBFile: def _create_imaging_plane_from_metadata(nwbfile: NWBFile, imaging_plane_metadata: dict) -> ImagingPlane: """ Private auxiliar function to create an ImagingPlane object from pynwb using the imaging_plane_metadata + Parameters ---------- nwbfile : NWBFile From 2af09947e213a83c0fd18c5a8d5e1107f79fbb2f Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Fri, 23 Sep 2022 21:00:17 +0200 Subject: [PATCH 21/25] full install again --- .readthedocs.yaml | 1 + docs/conf.py | 2 +- src/neuroconv/tools/roiextractors/roiextractors.py | 1 - 3 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 60ea831e7..8c8b525d3 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -22,3 +22,4 @@ python: path: . extra_requirements: - docs + - full diff --git a/docs/conf.py b/docs/conf.py index 2b6a5dcd7..b175334a9 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -3,7 +3,7 @@ from pathlib import Path sys.path.insert(0, str(Path(__file__).resolve().parents[1])) -from neuroconv.tools.roiextractors.imagingextractordatachunkiterator import GenericDataChunkIterator +from neuroconv.tools.roiextractors import * project = "NeuroConv" copyright = "2022, CatalystNeuro" diff --git a/src/neuroconv/tools/roiextractors/roiextractors.py b/src/neuroconv/tools/roiextractors/roiextractors.py index 3a9cd2eb3..869d5cfed 100644 --- a/src/neuroconv/tools/roiextractors/roiextractors.py +++ b/src/neuroconv/tools/roiextractors/roiextractors.py @@ -6,7 +6,6 @@ import psutil import numpy as np -from hdmf.common import VectorData from roiextractors import ImagingExtractor, SegmentationExtractor, MultiSegmentationExtractor from pynwb import NWBFile from pynwb.base import Images From 5702714d75916dc4b4fbe6444b405de9ddbe4daf Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Fri, 23 Sep 2022 21:06:15 +0200 Subject: [PATCH 22/25] another attempt --- .readthedocs.yaml | 1 - docs/api/tools.rst | 2 +- docs/conf.py | 1 - 3 files changed, 1 insertion(+), 3 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 8c8b525d3..60ea831e7 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -22,4 +22,3 @@ python: path: . extra_requirements: - docs - - full diff --git a/docs/api/tools.rst b/docs/api/tools.rst index 3ff527892..c45a70c54 100644 --- a/docs/api/tools.rst +++ b/docs/api/tools.rst @@ -5,6 +5,6 @@ Tools :maxdepth: 4 Spike Interface - tools.roiextractors + roiextractors tools.yaml_to_nwb_conversion tools.neo diff --git a/docs/conf.py b/docs/conf.py index b175334a9..dd434495d 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -3,7 +3,6 @@ from pathlib import Path sys.path.insert(0, str(Path(__file__).resolve().parents[1])) -from neuroconv.tools.roiextractors import * project = "NeuroConv" copyright = "2022, CatalystNeuro" From e29ea0a60fc1f83638b24fdd6dae4500d6516173 Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Fri, 23 Sep 2022 21:36:37 +0200 Subject: [PATCH 23/25] other test --- docs/api/tools.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/api/tools.rst b/docs/api/tools.rst index c45a70c54..3a71b68c7 100644 --- a/docs/api/tools.rst +++ b/docs/api/tools.rst @@ -4,7 +4,7 @@ Tools .. toctree:: :maxdepth: 4 - Spike Interface - roiextractors + tools.spikeinterface + ROI Extractors tools.yaml_to_nwb_conversion tools.neo From 931d4fbb133423109a539b71e6723cd2dcac52b6 Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Fri, 23 Sep 2022 21:45:32 +0200 Subject: [PATCH 24/25] final format --- docs/api/tools.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/api/tools.rst b/docs/api/tools.rst index 3a71b68c7..5b261df1f 100644 --- a/docs/api/tools.rst +++ b/docs/api/tools.rst @@ -5,6 +5,6 @@ Tools :maxdepth: 4 tools.spikeinterface - ROI Extractors + tools.roiextractors tools.yaml_to_nwb_conversion tools.neo From a1debf286c7c35ede7a5e2e1a1be8ba2bb387734 Mon Sep 17 00:00:00 2001 From: h-mayorquin Date: Fri, 23 Sep 2022 21:46:15 +0200 Subject: [PATCH 25/25] mynst parse out --- requirements-rtd.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/requirements-rtd.txt b/requirements-rtd.txt index 5cce1a405..9d9dcc9e0 100644 --- a/requirements-rtd.txt +++ b/requirements-rtd.txt @@ -1,4 +1,3 @@ -myst_parser==0.18.0 Jinja2<3.1 Sphinx==5.1.1 sphinx_rtd_theme==1.0.0