From 810751f3adecf133797fd3c41ec74fb6b21b81dd Mon Sep 17 00:00:00 2001 From: Garrett Michael Flynn Date: Thu, 28 Mar 2024 14:08:42 -0700 Subject: [PATCH 1/9] Provide next steps --- docs/conf_extlinks.py | 2 ++ docs/tutorials/multiple_sessions.rst | 2 +- docs/tutorials/next_steps.rst | 14 +++++++++++++- 3 files changed, 16 insertions(+), 2 deletions(-) diff --git a/docs/conf_extlinks.py b/docs/conf_extlinks.py index 89228803d..e474b8e31 100644 --- a/docs/conf_extlinks.py +++ b/docs/conf_extlinks.py @@ -5,6 +5,8 @@ "pynwb-docs": ("https://pynwb.readthedocs.io/en/stable/%s", "%s"), "matnwb-src": ("https://github.com/NeurodataWithoutBorders/matnwb/%s", "%s"), "nwb-overview": ("https://nwb-overview.readthedocs.io/en/latest/%s", "%s"), + "guide-issues": ("https://github.com/NeurodataWithoutBorders/nwb-guide/issues/%s", None), + "request-format-support": ("https://github.com/catalystneuro/neuroconv/issues/new?assignees=&labels=enhancement%2Cdata+interfaces&projects=&template=format_request.yml&title=%5BNew+Format%5D%3A+%s", "%s"), "path-expansion-guide": ("https://neuroconv.readthedocs.io/en/main/user_guide/expand_path.html%s", "%s"), "conda-install": ( "https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html#regular-installation%s", diff --git a/docs/tutorials/multiple_sessions.rst b/docs/tutorials/multiple_sessions.rst index 0821a5910..210e98c3e 100644 --- a/docs/tutorials/multiple_sessions.rst +++ b/docs/tutorials/multiple_sessions.rst @@ -21,7 +21,7 @@ This page helps you automatically identify source data for multiple subjects / s File locations are specified as **format strings** that define source data paths of each selected data format. .. note:: - Format strings are one component of NeuroConv's **path expansion language**, which has some nifty features for manually specifying complex paths. Complete documentation of the path expansion feature of NeuroConv can be found :path-expansion-guide:`here <>` . + Format strings are one component of NeuroConv's **path expansion language**, which has some nifty features for manually specifying complex paths. Complete documentation of the path expansion feature of NeuroConv can be found :path-expansion-guide:`here <>`. While you don’t have to specify a format strings for all of the pipeline’s data formats, we’re going to find all of our data here for this tutorial. diff --git a/docs/tutorials/next_steps.rst b/docs/tutorials/next_steps.rst index ce80155c6..d198631fe 100644 --- a/docs/tutorials/next_steps.rst +++ b/docs/tutorials/next_steps.rst @@ -1,3 +1,15 @@ What's Next? ======================================= -Coming soon... +Congratulations on finishing your first set of conversions using the NWB GUIDE! Feel free to try out your own data and/or +download relevant GIN datasets to test their support on the GUIDE. + +- **Ephys Data:** https://gin.g-node.org/NeuralEnsemble/ephy_testing_data +- **Ophys Data:** https://gin.g-node.org/CatalystNeuro/ophys_testing_data +- **Behavior Data:** https://gin.g-node.org/CatalystNeuro/behavior_testing_data + +Make sure to check out the rest of the :doc:`User Guide `. for more information on the GUIDE. + +To submit any feedback on the tutorial or your experience with the GUIDE, feel free to open an :guide-issues:`issue <>` on our GitHub page. + +If you do not see your data format listed on our :doc:`support table `. or the Data Formats page, please submit a request using :request-format-support:`this form <>`. + From 503ede4f66d59ff219e168b43f29174340a65228 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 28 Mar 2024 21:10:15 +0000 Subject: [PATCH 2/9] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- docs/tutorials/next_steps.rst | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/docs/tutorials/next_steps.rst b/docs/tutorials/next_steps.rst index d198631fe..24c9f5e81 100644 --- a/docs/tutorials/next_steps.rst +++ b/docs/tutorials/next_steps.rst @@ -1,7 +1,7 @@ What's Next? ======================================= -Congratulations on finishing your first set of conversions using the NWB GUIDE! Feel free to try out your own data and/or -download relevant GIN datasets to test their support on the GUIDE. +Congratulations on finishing your first set of conversions using the NWB GUIDE! Feel free to try out your own data and/or +download relevant GIN datasets to test their support on the GUIDE. - **Ephys Data:** https://gin.g-node.org/NeuralEnsemble/ephy_testing_data - **Ophys Data:** https://gin.g-node.org/CatalystNeuro/ophys_testing_data @@ -12,4 +12,3 @@ Make sure to check out the rest of the :doc:`User Guide `. for more info To submit any feedback on the tutorial or your experience with the GUIDE, feel free to open an :guide-issues:`issue <>` on our GitHub page. If you do not see your data format listed on our :doc:`support table `. or the Data Formats page, please submit a request using :request-format-support:`this form <>`. - From 395ffcf81e720eabc4ef468d72291297a1810663 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 3 Apr 2024 19:56:23 +0000 Subject: [PATCH 3/9] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- docs/tutorials/next_steps.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/tutorials/next_steps.rst b/docs/tutorials/next_steps.rst index a07bc7eff..bab6bce92 100644 --- a/docs/tutorials/next_steps.rst +++ b/docs/tutorials/next_steps.rst @@ -1,6 +1,6 @@ What's Next? ======================================= -Congratulations on finishing your first set of conversions using the NWB GUIDE! +Congratulations on finishing your first set of conversions using the NWB GUIDE! Make sure to check out the rest of the :doc:`User Guide `. for more information on the GUIDE. From b31dbcd3f1eac6b3176de52b93233dbecff58a45 Mon Sep 17 00:00:00 2001 From: Garrett Michael Flynn Date: Fri, 5 Apr 2024 07:48:38 -0700 Subject: [PATCH 4/9] Update next_steps.rst --- docs/tutorials/next_steps.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/tutorials/next_steps.rst b/docs/tutorials/next_steps.rst index bab6bce92..bd3c6c0c3 100644 --- a/docs/tutorials/next_steps.rst +++ b/docs/tutorials/next_steps.rst @@ -15,7 +15,7 @@ And finally, feel free to try out your own data and/or download relevant GIN dat - **Behavior Data:** https://gin.g-node.org/CatalystNeuro/behavior_testing_data Considerations for Real-World Use ---------------------------------------- +--------------------------------- When using the GUIDE to convert data from your own experiments, there are a few things to keep in mind: Choosing an Output Location From 606a86a32b231b8656e3695148a505481d7d1d70 Mon Sep 17 00:00:00 2001 From: Garrett Michael Flynn Date: Fri, 5 Apr 2024 08:09:35 -0700 Subject: [PATCH 5/9] Update next_steps.rst --- docs/tutorials/next_steps.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/tutorials/next_steps.rst b/docs/tutorials/next_steps.rst index bd3c6c0c3..3d1364d68 100644 --- a/docs/tutorials/next_steps.rst +++ b/docs/tutorials/next_steps.rst @@ -1,5 +1,5 @@ What's Next? -======================================= +============ Congratulations on finishing your first set of conversions using the NWB GUIDE! Make sure to check out the rest of the :doc:`User Guide `. for more information on the GUIDE. From 42ced45c079cc4493714188af93f3973f6e3b962 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Sat, 6 Apr 2024 14:45:47 -0400 Subject: [PATCH 6/9] Update docs/conf_extlinks.py --- docs/conf_extlinks.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/conf_extlinks.py b/docs/conf_extlinks.py index f23f772fa..0de4e096c 100644 --- a/docs/conf_extlinks.py +++ b/docs/conf_extlinks.py @@ -5,7 +5,7 @@ "pynwb-docs": ("https://pynwb.readthedocs.io/en/stable/%s", "%s"), "matnwb-src": ("https://github.com/NeurodataWithoutBorders/matnwb/%s", "%s"), "nwb-overview": ("https://nwb-overview.readthedocs.io/en/latest/%s", "%s"), - "guide-issues": ("https://github.com/NeurodataWithoutBorders/nwb-guide/issues/%s", None), + "guide-issues": ("https://github.com/NeurodataWithoutBorders/nwb-guide/issues/%s", "%s"), "request-format-support": ("https://github.com/catalystneuro/neuroconv/issues/new?assignees=&labels=enhancement%2Cdata+interfaces&projects=&template=format_request.yml&title=%5BNew+Format%5D%3A+%s", "%s"), "path-expansion-guide": ("https://neuroconv.readthedocs.io/en/main/user_guide/expand_path.html%s", "%s"), "dandi-staging": ("https://gui-staging.dandiarchive.org/%s", "%s"), From 88848e16890bd0538991a412564ffdfbe244899e Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Sat, 6 Apr 2024 14:47:36 -0400 Subject: [PATCH 7/9] Update docs/conf_extlinks.py --- docs/conf_extlinks.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/conf_extlinks.py b/docs/conf_extlinks.py index 0de4e096c..e6565f3c3 100644 --- a/docs/conf_extlinks.py +++ b/docs/conf_extlinks.py @@ -6,7 +6,7 @@ "matnwb-src": ("https://github.com/NeurodataWithoutBorders/matnwb/%s", "%s"), "nwb-overview": ("https://nwb-overview.readthedocs.io/en/latest/%s", "%s"), "guide-issues": ("https://github.com/NeurodataWithoutBorders/nwb-guide/issues/%s", "%s"), - "request-format-support": ("https://github.com/catalystneuro/neuroconv/issues/new?assignees=&labels=enhancement%2Cdata+interfaces&projects=&template=format_request.yml&title=%5BNew+Format%5D%3A+%s", "%s"), + "request-format-support": ("https://github.com/catalystneuro/neuroconv/issues/new?assignees=&labels=enhancement%%2Cdata+interfaces&projects=&template=format_request.yml&title=%%5BNew+Format%%5D%%3A+%s", "%s"), "path-expansion-guide": ("https://neuroconv.readthedocs.io/en/main/user_guide/expand_path.html%s", "%s"), "dandi-staging": ("https://gui-staging.dandiarchive.org/%s", "%s"), "dandi-archive": ("https://dandiarchive.org/%s", "%s"), From 35c8b7eeab316781871fb063c8e6c871f63bf147 Mon Sep 17 00:00:00 2001 From: Garrett Michael Flynn Date: Mon, 8 Apr 2024 11:50:04 -0700 Subject: [PATCH 8/9] Apply suggestions from code review Co-authored-by: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> --- docs/tutorials/next_steps.rst | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/docs/tutorials/next_steps.rst b/docs/tutorials/next_steps.rst index 3d1364d68..4969c9603 100644 --- a/docs/tutorials/next_steps.rst +++ b/docs/tutorials/next_steps.rst @@ -1,22 +1,16 @@ What's Next? ============ -Congratulations on finishing your first set of conversions using the NWB GUIDE! +Congratulations on finishing your first set of conversions using the NWB GUIDE using example data! The next big step is to make a pipeline for your own data. -Make sure to check out the rest of the :doc:`User Guide `. for more information on the GUIDE. To submit any feedback on the tutorial or your experience with the GUIDE, feel free to open an :guide-issues:`issue <>` on our GitHub page. -If you do not see your data format listed on our :doc:`support table `. or the Data Formats page, please submit a request using :request-format-support:`this form <>`. +If you do not see your data format listed on the Data Formats page or our :doc:`support table ` , please submit a request using :request-format-support:`this form <>`. -And finally, feel free to try out your own data and/or download relevant GIN datasets to test their support on the GUIDE. - -- **Ephys Data:** https://gin.g-node.org/NeuralEnsemble/ephy_testing_data -- **Ophys Data:** https://gin.g-node.org/CatalystNeuro/ophys_testing_data -- **Behavior Data:** https://gin.g-node.org/CatalystNeuro/behavior_testing_data Considerations for Real-World Use --------------------------------- -When using the GUIDE to convert data from your own experiments, there are a few things to keep in mind: +When using the GUIDE to convert data from your own experiments, there are a few things to keep in mind... Choosing an Output Location ^^^^^^^^^^^^^^^^^^^^^^^^^^^ From 4661538364026901b62411ad8e2ba22dd1416ee9 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Mon, 8 Apr 2024 22:37:52 -0400 Subject: [PATCH 9/9] Apply suggestions from code review --- docs/tutorials/next_steps.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/tutorials/next_steps.rst b/docs/tutorials/next_steps.rst index 4969c9603..01d9430b6 100644 --- a/docs/tutorials/next_steps.rst +++ b/docs/tutorials/next_steps.rst @@ -17,4 +17,5 @@ Choosing an Output Location Choosing a good output location is important for two reasons, namely **conversion speed** and **disk space**. 1. SSDs will be much faster than HDDs. We’d recommend moving the output location to an SSD if available. -2. If you don’t have much disk space available on your main drive, we recommend changing the output location to a drive that has ample space. +2. On-board (PCI slot) disk drives will be much faster than most conventional external USB drives. We recommend using an on-board disk drive whenever possible. +3. If you don’t have much disk space available on your main drive, we recommend changing the output location to a drive that has ample space.