From 4fe7c3950d9177b05d91c368d8a01c7dfe99bde5 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 16 Oct 2023 14:51:29 -0400 Subject: [PATCH 1/2] Re-record VCR tapes using newer versions of libraries MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit I believe that somehow some upgrade among ❯ wdiff -3 /tmp/f1 /tmp/f2 ====================================================================== [-06/github/cron/20231006T060312/0c1d4a0/Tests/5197/test-]{+07/github/cron/20231007T060245/0c1d4a0/Tests/5198/test+} ====================================================================== [-dependencies.txt:2023-10-06T06:05:18.6948668Z-] {+dependencies.txt:2023-10-07T06:04:51.1091526Z+} ====================================================================== [-boto3-1.28.61 botocore-1.31.61-] {+boto3-1.28.62 botocore-1.31.62+} ====================================================================== [-entrypoints-0.4-] ====================================================================== [-numcodecs-0.11.0-] {+numcodecs-0.12.0+} ====================================================================== [-urllib3-1.26.17-] {+urllib3-2.0.6+} ====================================================================== (so likely urllib3) lead to drastically different behavior which triggered VCR to try to not reuse prior tape but then subsequent dialog started to fail -- we got no json. As you can see in the diff we observe that now we do get json (as requested) recorded although previously it was some "binary". --- .../update_dandiset_from_doi/biorxiv.vcr.yaml | 244 +++++---- .../update_dandiset_from_doi/elife.vcr.yaml | 417 ++++++++------ .../jneurosci.vcr.yaml | 115 ++-- .../update_dandiset_from_doi/nature.vcr.yaml | 516 +++++++++++------- .../update_dandiset_from_doi/neuron.vcr.yaml | 383 +++++++------ 5 files changed, 976 insertions(+), 699 deletions(-) diff --git a/dandi/cli/tests/data/update_dandiset_from_doi/biorxiv.vcr.yaml b/dandi/cli/tests/data/update_dandiset_from_doi/biorxiv.vcr.yaml index b1e41b5cf..d927f0e6b 100644 --- a/dandi/cli/tests/data/update_dandiset_from_doi/biorxiv.vcr.yaml +++ b/dandi/cli/tests/data/update_dandiset_from_doi/biorxiv.vcr.yaml @@ -7,7 +7,7 @@ interactions: Connection: - keep-alive User-Agent: - - dandi/0.53.0+17.gc2f268f.dirty requests/2.28.2 CPython/3.11.3 + - dandi/0.56.2+5.ga0199fce.dirty requests/2.31.0 CPython/3.11.6 accept: - application/json method: GET @@ -21,7 +21,7 @@ interactions: CF-Cache-Status: - DYNAMIC CF-RAY: - - 7bd8e4c52e4a8215-IAD + - 81727698abd08c87-EWR Connection: - keep-alive Content-Length: @@ -29,19 +29,19 @@ interactions: Content-Type: - text/html;charset=utf-8 Date: - - Tue, 25 Apr 2023 19:11:45 GMT + - Mon, 16 Oct 2023 18:46:12 GMT NEL: - '{"success_fraction":0,"report_to":"cf-nel","max_age":604800}' Report-To: - - '{"endpoints":[{"url":"https:\/\/a.nel.cloudflare.com\/report\/v3?s=SJS2DJ8aGNbnuREMgLzy912O9dvXnZb2JaxDoyHf%2Bt89NGxInojmjPbXGHH6obSowIxEvUFRQOXV0D%2BUUd80pcYWDjAyb8upDquZQJH6wK90J%2BJbBnc2KRGYXFnlLN9zuBrwVX8%3D"}],"group":"cf-nel","max_age":604800}' + - '{"endpoints":[{"url":"https:\/\/a.nel.cloudflare.com\/report\/v3?s=EDGcAsnWWLKU8tj03j7uq9EVlzy6xYZBi3MtNGzcjVP%2FFeXDm5vKv0bmihqXEY6T5Fl2CaX6you4Hx5FgLmEu%2BEqJQP526h221xcfmW2wn6UJHsxA52UV%2FE%3D"}],"group":"cf-nel","max_age":604800}' Server: - cloudflare Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload alt-svc: - 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Reproducibility, however, has + been a concern in neuroscience, particularly for measurements of mouse behavior. + Here we show that a standardized task to probe decision-making in mice produces + reproducible results across multiple laboratories. We designed a task for + head-fixed mice that combines established assays of perceptual and value-based + decision making, and we standardized training protocol and experimental hardware, + software, and procedures. We trained 140 mice across seven laboratories in + three countries, and we collected 5 million mouse choices into a publicly + available database. Learning speed was variable across mice and laboratories, + but once training was complete there were no significant differences in behavior + across laboratories. Mice in different laboratories adopted similar reliance + on visual stimuli, on past successes and failures, and on estimates of stimulus + prior probability to guide their choices. These results reveal that a complex + mouse behavior can be successfully reproduced across multiple laboratories. + They establish a standard for reproducible rodent behavior, and provide an + unprecedented dataset and open-access tools to study decision-making in mice. + More generally, they indicate a path towards achieving reproducibility in + neuroscience through collaborative open-science approaches.<\/jats:p>","DOI":"10.1101\/2020.01.17.909838","type":"posted-content","created":{"date-parts":[[2020,1,18]],"date-time":"2020-01-18T09:15:13Z","timestamp":1579338913000},"source":"Crossref","is-referenced-by-count":12,"title":"Standardized + and reproducible measurement of decision-making in mice","prefix":"10.1101","author":[{"name":"The + International Brain Laboratory","sequence":"first","affiliation":[]},{"given":"Valeria","family":"Aguillon-Rodriguez","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-9650-8962","authenticated-orcid":false,"given":"Dora + E.","family":"Angelaki","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-5644-4124","authenticated-orcid":false,"given":"Hannah + M.","family":"Bayer","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0001-5228-6918","authenticated-orcid":false,"given":"Niccol\u00f2","family":"Bonacchi","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0003-4880-7682","authenticated-orcid":false,"given":"Matteo","family":"Carandini","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-9648-4761","authenticated-orcid":false,"given":"Fanny","family":"Cazettes","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-6849-5316","authenticated-orcid":false,"given":"Gaelle + A.","family":"Chapuis","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-3205-3794","authenticated-orcid":false,"given":"Anne + K.","family":"Churchland","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-3818-877X","authenticated-orcid":false,"given":"Yang","family":"Dan","sequence":"additional","affiliation":[]},{"given":"Eric + E. 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Most studies of area 2, + a proprioceptive area of somatosensory cortex, have simply compared neurons\u2019 + activities to the movement of the hand through space. Using motion tracking, + we sought to elaborate this relationship by characterizing how area 2 activity + relates to whole arm movements. We found that a whole-arm model, unlike classic + models, successfully predicted how features of neural activity changed as + monkeys reached to targets in two workspaces. However, when we then evaluated + this whole-arm model across active and passive movements, we found that many + neurons did not consistently represent the whole arm over both conditions. + These results suggest that 1) neural activity in area 2 includes representation + of the whole arm during reaching and 2) many of these neurons represented + limb state differently during active and passive movements.<\/jats:p>","DOI":"10.7554\/elife.48198","type":"journal-article","created":{"date-parts":[[2020,1,23]],"date-time":"2020-01-23T11:00:19Z","timestamp":1579777219000},"source":"Crossref","is-referenced-by-count":37,"title":"Area + 2 of primary somatosensory cortex encodes kinematics of the whole arm","prefix":"10.7554","volume":"9","author":[{"ORCID":"http:\/\/orcid.org\/0000-0002-5934-919X","authenticated-orcid":true,"given":"Raeed + H","family":"Chowdhury","sequence":"first","affiliation":[{"name":"Department + of Biomedical Engineering, Northwestern University, Evanston, United States"},{"name":"Systems + Neuroscience Institute, University of Pittsburgh, Pittsburgh, United States"}]},{"ORCID":"http:\/\/orcid.org\/0000-0003-2906-115X","authenticated-orcid":true,"given":"Joshua + I","family":"Glaser","sequence":"additional","affiliation":[{"name":"Interdepartmental + Neuroscience Program, Northwestern University, Chicago, United States"},{"name":"Department + of Statistics, Columbia University, New York, United States"},{"name":"Zuckerman + Mind Brain Behavior Institute, Columbia University, New York, United States"}]},{"ORCID":"http:\/\/orcid.org\/0000-0001-8675-7140","authenticated-orcid":true,"given":"Lee + E","family":"Miller","sequence":"additional","affiliation":[{"name":"Department + of Biomedical Engineering, Northwestern University, Evanston, United States"},{"name":"Department + of Physiology, Northwestern University, Chicago, United States"},{"name":"Department + of Physical Medicine and Rehabilitation, Northwestern University, Chicago, + United 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Especially, intermediate + variables of learning models estimated from behavioral data, such as the expectation + of reward for each candidate choice (action value), have been used in searches + for the neural correlates of computational elements in learning and decision + making. The aims of the present study are as follows: (1) to test which computational + model best captures the choice learning process in animals and (2) to elucidate + how action values are represented in different parts of the corticobasal ganglia + circuit. We compared different behavioral learning algorithms to predict the + choice sequences generated by rats during a free-choice task and analyzed + associated neural activity in the nucleus accumbens (NAc) and ventral pallidum + (VP). The major findings of this study were as follows: (1) modified versions + of an action\u2013value learning model captured a variety of choice strategies + of rats, including win-stay\u2013lose-switch and persevering behavior, and + predicted rats'' choice sequences better than the best multistep Markov model; + and (2) information about action values and future actions was coded in both + the NAc and VP, but was less dominant than information about trial types, + selected actions, and reward outcome. The results of our model-based analysis + suggest that the primary role of the NAc and VP is to monitor information + important for updating choice behaviors. Information represented in the NAc + and VP might contribute to a choice mechanism that is situated elsewhere.<\/jats:p>","DOI":"10.1523\/jneurosci.6157-08.2009","type":"journal-article","created":{"date-parts":[[2009,8,5]],"date-time":"2009-08-05T17:33:40Z","timestamp":1249493620000},"page":"9861-9874","source":"Crossref","is-referenced-by-count":190,"title":"Validation + of Decision-Making Models and Analysis of Decision Variables in the Rat Basal + 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To investigate how population-level heading responses + are aligned to visual input, we recorded from retrosplenial cortex (RSC) of + head-fixed mice in a moving environment using two-photon calcium imaging. + We show that RSC neurons are tuned to the animal\u2019s relative orientation + in the environment, even in the absence of head movement. Next, we found that + RSC receives functionally distinct projections from visual and thalamic areas + and contains several functional classes of neurons. While some functional + classes mirror RSC inputs, a newly discovered class coregisters visual and + thalamic signals. Finally, decoding analyses reveal unique contributions to + heading from each class. Our results suggest an RSC circuit for anchoring + heading representations to environmental visual landmarks.<\/jats:p>","DOI":"10.1038\/s41467-023-37704-5","type":"journal-article","created":{"date-parts":[[2023,4,8]],"date-time":"2023-04-08T14:02:45Z","timestamp":1680962565000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":"Coregistration + of heading to visual cues in retrosplenial cortex","prefix":"10.1038","volume":"14","author":[{"given":"Kevin + K.","family":"Sit","sequence":"first","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-5366-8501","authenticated-orcid":false,"given":"Michael + J.","family":"Goard","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,4,8]]},"reference":[{"key":"37704_CR1","doi-asserted-by":"publisher","first-page":"849","DOI":"10.1126\/science.aal4835","volume":"356","author":"SS + Kim","year":"2017","unstructured":"Kim, S. 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GMT link: - ; rel="canonical", ; version="vor"; type="text/xml"; rel="item", ; From 25bd01c9520d7897c609a9a657fa5eb19fcd6c68 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 31 Oct 2023 20:34:36 -0400 Subject: [PATCH 2/2] Look forward -- XFail the test on older Pythons --- dandi/cli/tests/test_service_scripts.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/dandi/cli/tests/test_service_scripts.py b/dandi/cli/tests/test_service_scripts.py index f37a43299..dcbf5791c 100644 --- a/dandi/cli/tests/test_service_scripts.py +++ b/dandi/cli/tests/test_service_scripts.py @@ -5,6 +5,7 @@ import os from pathlib import Path import re +import sys import anys from click.testing import CliRunner @@ -48,6 +49,10 @@ def record_only_doi_requests(request): return None +@pytest.mark.xfail( + sys.version_info < (3, 10), + reason="Some difference in VCR tape: https://github.com/dandi/dandi-cli/pull/1337", +) @pytest.mark.parametrize( "doi,name", [