fix: adds alternate lookup if base lookup fails #896
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holtjma
changed the title
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Not sure what those failures are, they seem to be related to DESeq2. I think it's unrelated to the changes here, but I could be wrong. |
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@bioconda/core Not sure who to ping here, but hoping for feedback on the PR content and debugging that test (seemingly related to bioconductor). |
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Wow, yeah that DESeq2 failure is definitely not your fault, I suspect bioconductor has removed the file. |
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@johanneskoester @mbargull Any thoughts on this PR? |
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@johanneskoester @mbargull @dpryan79 Circling back on this, any thoughts on the functional changes and/or fixing the test? Happy to look into making the changes, just need to know what's missing here. |
johanneskoester
approved these changes
Jun 19, 2023
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@johanneskoester I fixed that previous error by just bumping the versions (assuming this is fine). However, there's some new error in the OSX tests (this appears to have been added after the master branch merge). I took a quick look, but it's not obvious to me what's happening there. |
dpryan79
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Jul 6, 2023
🤖 I have created a release \*beep\* \*boop\* --- ### [2.3.3](https://www.github.com/bioconda/bioconda-utils/compare/v2.3.2...v2.3.3) (2023-07-06) ### Bug Fixes * adds alternate lookup if base lookup fails ([#896](https://www.github.com/bioconda/bioconda-utils/issues/896)) ([17a1475](https://www.github.com/bioconda/bioconda-utils/commit/17a147508a64bdafb6031c05a75724b25669ec8d)) * update r-base pinning ([#901](https://www.github.com/bioconda/bioconda-utils/issues/901)) ([54d8702](https://www.github.com/bioconda/bioconda-utils/commit/54d870205d823b6f292df5258b980cbbaa97df77)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
This was referenced Jul 25, 2023
johanneskoester
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Aug 16, 2023
This is basically a patch to fix a new issue (described here: bioconda/bioconda-recipes#42176) that was introduced by myself here: #896. The primary cause is that the GitHub API is rate limited (which I was not aware of), so autobump basically blows through the limits quickly and then subsequent calls automatically fail. Of course, this means that the tools we were hoping to see get autobumped are not. This patch basically removes the original patch (which uses a single GitHub API call) and replaces it with an approach that basically "expands" the release webpage to find the assets. See #895 for more details on how the URLs are masked and the expansion pattern. Couple other notes: * I added an `IncludeFragmentParser` that is basically identical to the `HrefParser` except it is looking for tags with this pattern: `<include-fragment src="http://url/of/interest" ...>` * The general expansion logic is: * Pull the full release page * Search for `<include-fragment ...>` tags * Iteratively pull these looking for the main link URL of interest * Break the above iteration early if the current version is identified * This should no longer use the GitHub API, I'm unaware of other rate limiters for these URLs (🤞that none are hidden...) Pinging @dpryan79 and @johanneskoester as you both reviewed the last related PR. Sorry that the previous PR injected a rate limit issue! EDIT: I forgot, I have tested these on both `hiphase` and `pbfusion` recipes, the diff of the results are here and match our current expectations: ``` (bioconda)$ git diff diff --git a/recipes/hiphase/meta.yaml b/recipes/hiphase/meta.yaml index 38b939bf9f..b5d2503597 100644 --- a/recipes/hiphase/meta.yaml +++ b/recipes/hiphase/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hiphase" %} -{% set version = "0.10.0" %} -{% set hiphase_sha256 = "e22d3530a395bd218bd4634537f5b3c31a82cd8155849291c69d81c48f0c58fe" %} +{% set version = "0.10.2" %} +{% set hiphase_sha256 = "2a20fc437ab5c0f2437246e8a36e7590c68f5ae5caa0cecb8e85a371f5357c6c" %} package: name: {{ name }} diff --git a/recipes/pbfusion/meta.yaml b/recipes/pbfusion/meta.yaml index 781ada3413..ca69e87d0f 100644 --- a/recipes/pbfusion/meta.yaml +++ b/recipes/pbfusion/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pbfusion" %} -{% set version = "0.2.2" %} -{% set pbfusion_sha256 = "3390adbeb8550265fcf4fad89dad80740cc368e96d10f3b23bb19ef001ffd081" %} +{% set version = "0.3.0" %} +{% set pbfusion_sha256 = "ef9767af7e82bd1e664711e7521d7a8370a41f101cccf1db4a58895d9f88934c" %} package: name: {{ name }} ```
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This is a first pass attempt at fixing #895.
Main changes are updating the GithubRelease hoster to look for alternate paths via the GitHub API. The API sends a JSON response (example: https://api.github.com/repos/PacificBiosciences/HiPhase/releases) that contains each release along with a list of assets. The assets are searched for files that match the provides pattern. Currently, this first pass puts this as a backup to the main one (which I think is always failing now). I also did not update the tests, I think someone may have a better idea of how to do that. Happy to help push this further, but wanted to get the ball rolling.