From 1c8dc443f50ad45a5965c95af884e44497170bf2 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Sun, 22 Dec 2024 16:25:54 -0800 Subject: [PATCH 1/8] Fix broken hdmf-zarr doc links --- docs/source/conf_extlinks.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/conf_extlinks.py b/docs/source/conf_extlinks.py index f2059aa..e80a135 100644 --- a/docs/source/conf_extlinks.py +++ b/docs/source/conf_extlinks.py @@ -30,7 +30,7 @@ 'nwb-schema-src': ('https://github.com/NeurodataWithoutBorders/nwb-schema/%s', '%s'), 'hdmf-common-schema-docs': ('https://hdmf-common-schema.readthedocs.io/en/stable/%s', '%s'), 'hdmf-common-schema-src': ('https://github.com/hdmf-dev/hdmf-common-schema/%s', '%s'), - 'hdmf-z-docs': ('https://hdmf-zarr.readthedocs.io/en/latest/%s', '%s'), + 'hdmf-z-docs': ('https://hdmf-zarr.readthedocs.io/en/stable/%s', '%s'), 'hdmf-z-src': ('https://github.com/hdmf-dev/hdmf-zarr/%s', '%s'), 'nwb-github-org': ('https://github.com/NeurodataWithoutBorders/%s', '%s'), 'hdmf-github-org': ('https://github.com/hdmf-dev/%s', '%s'), @@ -66,7 +66,7 @@ 'matplotlib': ('https://matplotlib.org/stable/', None), 'h5py': ('https://docs.h5py.org/en/latest/', None), 'hdmf': ('https://hdmf.readthedocs.io/en/stable/', None), - 'hdmf-z': ('https://hdmf-zarr.readthedocs.io/en/latest/', None), + 'hdmf-z': ('https://hdmf-zarr.readthedocs.io/en/stable/', None), 'pynwb': ('https://pynwb.readthedocs.io/en/stable/', None), 'pandas': ('https://pandas.pydata.org/pandas-docs/stable/', None), 'neuroconv': ('https://neuroconv.readthedocs.io/en/main/', None), From db2ea572a1f5f95d9384a2e50330ed0c41be6473 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Mon, 23 Dec 2024 13:48:49 -0800 Subject: [PATCH 2/8] Fix matnwb doc links --- docs/source/conf_extlinks.py | 2 +- docs/source/conversion_tutorial/03_nwb_apis.rst | 8 ++++---- docs/source/core_tools/core_tools_home.rst | 2 +- docs/source/file_read/file_read.rst | 2 +- docs/source/file_read/matnwb/dynamictable.rst | 2 +- docs/source/file_read/matnwb/untyped.rst | 2 +- docs/source/intro_to_nwb/4_apis.rst | 2 +- 7 files changed, 10 insertions(+), 10 deletions(-) diff --git a/docs/source/conf_extlinks.py b/docs/source/conf_extlinks.py index e80a135..a1c732d 100644 --- a/docs/source/conf_extlinks.py +++ b/docs/source/conf_extlinks.py @@ -14,7 +14,7 @@ 'hdmf-src': ('https://github.com/hdmf-dev/hdmf/%s', '%s'), 'hdmf-specification-language': ('https://hdmf-schema-language.readthedocs.io/en/latest/%s', '%s'), 'matnwb-src': ('https://github.com/NeurodataWithoutBorders/matnwb/%s', '%s'), - 'matnwb-docs': ('https://neurodatawithoutborders.github.io/matnwb/%s', '%s'), + 'matnwb-docs': ('https://matnwb.readthedocs.io/en/latest/%s', '%s'), 'neuroconv-docs': ('https://neuroconv.readthedocs.io/en/main/%s', '%s'), 'neuroconv-src': ('https://github.com/catalystneuro/neuroconv/%s', '%s'), 'nwbinspector-docs': ('https://nwbinspector.readthedocs.io/en/dev/%s', '%s'), diff --git a/docs/source/conversion_tutorial/03_nwb_apis.rst b/docs/source/conversion_tutorial/03_nwb_apis.rst index 712f8e9..19b31b9 100644 --- a/docs/source/conversion_tutorial/03_nwb_apis.rst +++ b/docs/source/conversion_tutorial/03_nwb_apis.rst @@ -29,24 +29,24 @@ modality: `23 min video `__ - - `tutorial `__ + - `tutorial `__ `46 min video `__ * - Writing intracellular electrophysiology - `tutorial `__ - - `tutorial `__ + - `tutorial `__ * - Writing calcium imaging - `tutorial `__ `31 min video `__ - - `tutorial `__ + - `tutorial `__ `39 min video `__ * - Advanced I/O - `tutorials `__ `26 min video `__ - - `tutorial `__ + - `tutorial `__ `16 min video `__ diff --git a/docs/source/core_tools/core_tools_home.rst b/docs/source/core_tools/core_tools_home.rst index 4720ee6..2989425 100644 --- a/docs/source/core_tools/core_tools_home.rst +++ b/docs/source/core_tools/core_tools_home.rst @@ -31,7 +31,7 @@ The NWB reference APIs provide full support for reading and writing all componen :class: align-left, no-scaled-link :width: 100 -:matnwb-docs:`MatNWB <>` is a MATLAB library for reading and writing NWB files. :bdg-link-primary:`Docs ` :bdg-link-primary:`Tutorials ` :bdg-link-primary:`Source ` +:matnwb-docs:`MatNWB <>` is a MATLAB library for reading and writing NWB files. :bdg-link-primary:`Docs ` :bdg-link-primary:`Tutorials ` :bdg-link-primary:`Source ` .. raw:: html diff --git a/docs/source/file_read/file_read.rst b/docs/source/file_read/file_read.rst index 1b8ee18..92657f4 100644 --- a/docs/source/file_read/file_read.rst +++ b/docs/source/file_read/file_read.rst @@ -3,7 +3,7 @@ Reading NWB Files ================== -This section provides an introduction on how to read NWB files in Python using PyNWB and Matlab using MatNWB. If you are interested in converting your data to NWB, then please see the :neuroconv-docs:`NeuroConv User Guide ` as well as for more in-depth tutorials visit the :pynwb-docs:`PyNWB ` and :matnwb-docs:`MatNWB <#tutorials>` tutorials and documentation. +This section provides an introduction on how to read NWB files in Python using PyNWB and Matlab using MatNWB. If you are interested in converting your data to NWB, then please see the :neuroconv-docs:`NeuroConv User Guide ` as well as for more in-depth tutorials visit the :pynwb-docs:`PyNWB ` and :matnwb-docs:`MatNWB ` tutorials and documentation. Reading With PyNWB ~~~~~~~~~~~~~~~~~~ diff --git a/docs/source/file_read/matnwb/dynamictable.rst b/docs/source/file_read/matnwb/dynamictable.rst index d811126..2f1fda1 100644 --- a/docs/source/file_read/matnwb/dynamictable.rst +++ b/docs/source/file_read/matnwb/dynamictable.rst @@ -34,4 +34,4 @@ Finally, if you prefer to select using your custom ``id`` column, you can specif tableData = dynamicTable.getRow(, 'useId', true); -For more information regarding Dynamic Tables in MatNWB as well as information regarding writing data to them, please see the `MatNWB DynamicTables Tutorial `_. +For more information regarding Dynamic Tables in MatNWB as well as information regarding writing data to them, please see the `MatNWB DynamicTables Tutorial `_. diff --git a/docs/source/file_read/matnwb/untyped.rst b/docs/source/file_read/matnwb/untyped.rst index 2cfc439..40ebade 100644 --- a/docs/source/file_read/matnwb/untyped.rst +++ b/docs/source/file_read/matnwb/untyped.rst @@ -35,7 +35,7 @@ DataStubs and DataPipes .. image:: /img/matnwb_datastub.png -**DataPipes** are similar to DataStubs in that they allow you to load data from disk; however, they also provide a wide array of features that allow the user to write data to disk, either by streaming parts of data in at a time or by compressing the data before writing. The DataPipe is an advanced type and users looking to leverage DataPipe's capabilities to stream/iteratively write or compress data should read the `Advanced Data Write Tutorial `_. +**DataPipes** are similar to DataStubs in that they allow you to load data from disk; however, they also provide a wide array of features that allow the user to write data to disk, either by streaming parts of data in at a time or by compressing the data before writing. The DataPipe is an advanced type and users looking to leverage DataPipe's capabilities to stream/iteratively write or compress data should read the `Advanced Data Write Tutorial `_. .. _matnwb-read-untyped-links-views: diff --git a/docs/source/intro_to_nwb/4_apis.rst b/docs/source/intro_to_nwb/4_apis.rst index 7a311ae..f0c1331 100644 --- a/docs/source/intro_to_nwb/4_apis.rst +++ b/docs/source/intro_to_nwb/4_apis.rst @@ -45,7 +45,7 @@ researchers and developers interested in using NWB and in learning more about th A growing collection of :ref:`analysistools-home` (gray) developed by the neurophysiology community along with a broad range of :ref:`core tools ` (red) help users with conversion, extension, validation and use of -NWB data files. Commonly, these tools build on the :pynwb-docs:`PyNWB (Python) <>` and :matnwb-docs:`MatNWB (Matlab) <>` +NWB data files. Commonly, these tools build on the :pynwb-docs:`PyNWB (Python) <>` and :matnwb-docs:`MatNWB (MATLAB) <>` reference APIs (lilac) to read and write NWB files. Each of the APIs and tools provides their own in-depth tutorials and documentation to help guide users in adopting and using the software. From 730107dbedca916f63a5bbaa5e73e4544c415931 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Mon, 23 Dec 2024 14:01:59 -0800 Subject: [PATCH 3/8] Fix matnwb link --- docs/source/faq.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/faq.rst b/docs/source/faq.rst index 508678c..62260c4 100644 --- a/docs/source/faq.rst +++ b/docs/source/faq.rst @@ -29,7 +29,7 @@ See the :ref:`install_users` for details. How do I install MatNWB? ------------------------ -See the :matnwb-docs:`MatNWB documentation <#setup>` for details. +See the :matnwb-docs:`MatNWB documentation ` for details. What is the difference between PyNWB and nwb-schema? ---------------------------------------------------- From 76672cbb39775a76ca8ad8a65477189d619824e0 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Mon, 23 Dec 2024 14:06:42 -0800 Subject: [PATCH 4/8] Workaround for mathworks links --- docs/source/conf.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 1fdc28a..c32fdba 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -75,8 +75,14 @@ linkcheck_ignore = [ "https://crates.io/crates/nwbview", r"https://.*\.incf\.org/.*", # temporary ignore until SSL certificate issue is resolved - ] +# some websites seem to block the sphinx link checker +linkcheck_request_headers = { + r'https://www.mathworks.com/': { + 'User-Agent': 'Mozilla/5.0 (X11; Linux i686; rv:124.0) Gecko/20100101 Firefox/124.0' + }, +} + # -- Build the nwb project analytics in the current directory build_project_analytics(target_dir=os.path.dirname(__file__)) From 7c18cf5ce6c19541b9a8854ae131ffadd65259e4 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Mon, 23 Dec 2024 14:38:22 -0800 Subject: [PATCH 5/8] Fix link, try a different user agent --- docs/source/conf.py | 2 +- docs/source/faq.rst | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index c32fdba..ec112d6 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -80,7 +80,7 @@ # some websites seem to block the sphinx link checker linkcheck_request_headers = { r'https://www.mathworks.com/': { - 'User-Agent': 'Mozilla/5.0 (X11; Linux i686; rv:124.0) Gecko/20100101 Firefox/124.0' + 'User-Agent': 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/131.0.0.0 Safari/537.36' }, } diff --git a/docs/source/faq.rst b/docs/source/faq.rst index 62260c4..5978650 100644 --- a/docs/source/faq.rst +++ b/docs/source/faq.rst @@ -29,7 +29,7 @@ See the :ref:`install_users` for details. How do I install MatNWB? ------------------------ -See the :matnwb-docs:`MatNWB documentation ` for details. +See the :matnwb-docs:`MatNWB documentation ` for details. What is the difference between PyNWB and nwb-schema? ---------------------------------------------------- From 12ebd41473f4a07177f9983914f979ca4ec35c81 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Mon, 23 Dec 2024 16:01:58 -0800 Subject: [PATCH 6/8] Remove not working mathworks workaround --- docs/source/conf.py | 7 ------- 1 file changed, 7 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index ec112d6..23fdfe1 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -77,12 +77,5 @@ r"https://.*\.incf\.org/.*", # temporary ignore until SSL certificate issue is resolved ] -# some websites seem to block the sphinx link checker -linkcheck_request_headers = { - r'https://www.mathworks.com/': { - 'User-Agent': 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/131.0.0.0 Safari/537.36' - }, -} - # -- Build the nwb project analytics in the current directory build_project_analytics(target_dir=os.path.dirname(__file__)) From 8a4e658418d11d86fb88780166e7e6231e553230 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Thu, 2 Jan 2025 17:33:57 -0800 Subject: [PATCH 7/8] Ignore mathworks URLs --- docs/source/conf.py | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/source/conf.py b/docs/source/conf.py index 23fdfe1..9c67fd0 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -75,6 +75,7 @@ linkcheck_ignore = [ "https://crates.io/crates/nwbview", r"https://.*\.incf\.org/.*", # temporary ignore until SSL certificate issue is resolved + "https://www.mathworks.com/.*", # ignore because linkchecker receives 403 error no matter what we try ] # -- Build the nwb project analytics in the current directory From 3f1724c17d04e894a33b95b297cdf2a614708e96 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Thu, 2 Jan 2025 17:34:19 -0800 Subject: [PATCH 8/8] Address warning about html_theme --- docs/source/conf.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 9c67fd0..38cd448 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -38,9 +38,6 @@ templates_path = ['_templates'] -# -- Options for HTML output -html_theme = 'sphinx_rtd_theme' - # -- Options for EPUB output epub_show_urls = 'footnote'