ci: move pandas/scipy stubs to pypi deps - #11370

Merged
keewis merged 3 commits into
pydata:mainfrom
maxrjones:fix/mypy-type-envs
Jun 3, 2026
Merged

ci: move pandas/scipy stubs to pypi deps#11370
keewis merged 3 commits into
pydata:mainfrom
maxrjones:fix/mypy-type-envs

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Description

This PR moves the pandas/scipy stubs to pypi deps so that the test-nightly workflow succeeds, as discussed in #11279. With the previous version, mypy in test-nightly floated to >2 and lacked pip in the env , which caused a lot of failures.

Checklist

  • Closes #xxxx
  • Tests added
  • User visible changes (including notable bug fixes) are documented in whats-new.rst
  • New functions/methods are listed in api.rst

AI Disclosure

  • This PR contains AI-generated content.
    • I have tested any AI-generated content in my PR.
    • I take responsibility for any AI-generated content in my PR. Tools: {e.g., Claude, Codex, GitHub Copilot, ChatGPT, etc.}

@keewiskeewis added the run-upstream Run upstream CI label Jun 2, 2026
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cc @Illviljan

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looks good to me, but why does this resolve >100 tests that are failing on main?

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why does this resolve >100 tests that are failing on main?

Which workflow are you looking at?

@keewis

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the only one that's failing: https://github.com/pydata/xarray/actions/runs/26844047852/job/79159106197?pr=11370 This shows 59 failing tests, compared to 176 in the latest scheduled run on main: https://github.com/pydata/xarray/actions/runs/26791334945/job/78978472251

I think the reason for that is that numpy is installed through conda and not from the scientific-python nightly wheels repo.

@github-actionsgithub-actionsBot added the Automation Github bots, testing workflows, release automation label Jun 2, 2026
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the only one that's failing: pydata/xarray/actions/runs/26844047852/job/79159106197?pr=11370 This shows 59 failing tests, compared to 176 in the latest scheduled run on main: pydata/xarray/actions/runs/26791334945/job/78978472251

I think the reason for that is that numpy is installed through conda and not from the scientific-python nightly wheels repo.

Good catch, thanks for noticing that. It turns out the stubs require a released numpy which bumps numpy off the nightly wheels:

  • scipy-stubs (via optype -> numpy-typing-compat) requires numpy<2.5
  • pandas-stubes requires numpy<=2.3.5
  • types-networkx pulls a conda numpy

It's not possible to have an upstream environment with nightly numpy and typing across the dependency suite. I have therefore split the upstream test run and upstream type checking:

  • test-nightly (the pytest just) stays stub-free and keeps the nightly numpy restoring the failures
  • mypy-upstream (a new env for mypy-upstream-dev) carries the typing toolchain + stubs.

The mypy-upstream uses a released numpy, but I don't see a way around that given the pins.

@keewis

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I was thinking that we'd put all the types-* / *-stubs packages in pypi-packages (since that's what mypy would do to install these, anyways), but indeed it appears that numpy-typing-compat has an upper bound through the version of optype (neither pandas-stubs nor types-networkx appear to have an upper bound on numpy, but installing them through conda will introduce an artificial pin on numpy, and potentially the same with hypothesis)

@maxrjones

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I was thinking that we'd put all the types-* / *-stubs packages in pypi-packages (since that's what mypy would do to install these, anyways), but indeed it appears that numpy-typing-compat has an upper bound through the version of optype (neither pandas-stubs nor types-networkx appear to have an upper bound on numpy, but installing them through conda will introduce an artificial pin on numpy, and potentially the same with hypothesis)

yes, it's messy 😞 Are you alright with the current approach in this PR (not having numpy nightly in the mypy checks)?

@keewis

keewis commented Jun 3, 2026

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I'm fine with it personally so I'll go ahead and merge. I've opened #11371 to keep track of the issue.

@keewis
keewis merged commit d93d0ab into pydata:mainJun 3, 2026
42 of 43 checks passed
sdiebolt pushed a commit to sdiebolt/xarray that referenced this pull request Aug 12, 2026
* ci: move pandas/scipy stubs to pypi deps so typing works in test-nightly
* ci: confine pypi stubs to nightly env
* ci: type-check the dev stack in a dedicated mypy-upstream env
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ci: move pandas/scipy stubs to pypi deps - #11370

Merged
keewis merged 3 commits into
pydata:mainfrom
maxrjones:fix/mypy-type-envs
Jun 3, 2026
Merged

ci: move pandas/scipy stubs to pypi deps#11370
keewis merged 3 commits into
pydata:mainfrom
maxrjones:fix/mypy-type-envs

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@maxrjones

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Description

This PR moves the pandas/scipy stubs to pypi deps so that the test-nightly workflow succeeds, as discussed in #11279. With the previous version, mypy in test-nightly floated to >2 and lacked pip in the env , which caused a lot of failures.

Checklist

  • Closes #xxxx
  • Tests added
  • User visible changes (including notable bug fixes) are documented in whats-new.rst
  • New functions/methods are listed in api.rst

AI Disclosure

  • This PR contains AI-generated content.
    • I have tested any AI-generated content in my PR.
    • I take responsibility for any AI-generated content in my PR. Tools: {e.g., Claude, Codex, GitHub Copilot, ChatGPT, etc.}

@keewiskeewis added the run-upstream Run upstream CI label Jun 2, 2026
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cc @Illviljan

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looks good to me, but why does this resolve >100 tests that are failing on main?

@maxrjones

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why does this resolve >100 tests that are failing on main?

Which workflow are you looking at?

@keewis

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the only one that's failing: https://github.com/pydata/xarray/actions/runs/26844047852/job/79159106197?pr=11370 This shows 59 failing tests, compared to 176 in the latest scheduled run on main: https://github.com/pydata/xarray/actions/runs/26791334945/job/78978472251

I think the reason for that is that numpy is installed through conda and not from the scientific-python nightly wheels repo.

@github-actionsgithub-actionsBot added the Automation Github bots, testing workflows, release automation label Jun 2, 2026
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the only one that's failing: pydata/xarray/actions/runs/26844047852/job/79159106197?pr=11370 This shows 59 failing tests, compared to 176 in the latest scheduled run on main: pydata/xarray/actions/runs/26791334945/job/78978472251

I think the reason for that is that numpy is installed through conda and not from the scientific-python nightly wheels repo.

Good catch, thanks for noticing that. It turns out the stubs require a released numpy which bumps numpy off the nightly wheels:

  • scipy-stubs (via optype -> numpy-typing-compat) requires numpy<2.5
  • pandas-stubes requires numpy<=2.3.5
  • types-networkx pulls a conda numpy

It's not possible to have an upstream environment with nightly numpy and typing across the dependency suite. I have therefore split the upstream test run and upstream type checking:

  • test-nightly (the pytest just) stays stub-free and keeps the nightly numpy restoring the failures
  • mypy-upstream (a new env for mypy-upstream-dev) carries the typing toolchain + stubs.

The mypy-upstream uses a released numpy, but I don't see a way around that given the pins.

@keewis

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I was thinking that we'd put all the types-* / *-stubs packages in pypi-packages (since that's what mypy would do to install these, anyways), but indeed it appears that numpy-typing-compat has an upper bound through the version of optype (neither pandas-stubs nor types-networkx appear to have an upper bound on numpy, but installing them through conda will introduce an artificial pin on numpy, and potentially the same with hypothesis)

@maxrjones

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I was thinking that we'd put all the types-* / *-stubs packages in pypi-packages (since that's what mypy would do to install these, anyways), but indeed it appears that numpy-typing-compat has an upper bound through the version of optype (neither pandas-stubs nor types-networkx appear to have an upper bound on numpy, but installing them through conda will introduce an artificial pin on numpy, and potentially the same with hypothesis)

yes, it's messy 😞 Are you alright with the current approach in this PR (not having numpy nightly in the mypy checks)?

@keewis

keewis commented Jun 3, 2026

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I'm fine with it personally so I'll go ahead and merge. I've opened #11371 to keep track of the issue.

@keewis
keewis merged commit d93d0ab into pydata:mainJun 3, 2026
42 of 43 checks passed
sdiebolt pushed a commit to sdiebolt/xarray that referenced this pull request Aug 12, 2026
* ci: move pandas/scipy stubs to pypi deps so typing works in test-nightly
* ci: confine pypi stubs to nightly env
* ci: type-check the dev stack in a dedicated mypy-upstream env
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ci: move pandas/scipy stubs to pypi deps - #11370

Merged
keewis merged 3 commits into
pydata:mainfrom
maxrjones:fix/mypy-type-envs
Jun 3, 2026
Merged

ci: move pandas/scipy stubs to pypi deps#11370
keewis merged 3 commits into
pydata:mainfrom
maxrjones:fix/mypy-type-envs

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@maxrjones

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Description

This PR moves the pandas/scipy stubs to pypi deps so that the test-nightly workflow succeeds, as discussed in #11279. With the previous version, mypy in test-nightly floated to >2 and lacked pip in the env , which caused a lot of failures.

Checklist

  • Closes #xxxx
  • Tests added
  • User visible changes (including notable bug fixes) are documented in whats-new.rst
  • New functions/methods are listed in api.rst

AI Disclosure

  • This PR contains AI-generated content.
    • I have tested any AI-generated content in my PR.
    • I take responsibility for any AI-generated content in my PR. Tools: {e.g., Claude, Codex, GitHub Copilot, ChatGPT, etc.}

@keewiskeewis added the run-upstream Run upstream CI label Jun 2, 2026
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cc @Illviljan

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looks good to me, but why does this resolve >100 tests that are failing on main?

@maxrjones

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why does this resolve >100 tests that are failing on main?

Which workflow are you looking at?

@keewis

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the only one that's failing: https://github.com/pydata/xarray/actions/runs/26844047852/job/79159106197?pr=11370 This shows 59 failing tests, compared to 176 in the latest scheduled run on main: https://github.com/pydata/xarray/actions/runs/26791334945/job/78978472251

I think the reason for that is that numpy is installed through conda and not from the scientific-python nightly wheels repo.

@github-actionsgithub-actionsBot added the Automation Github bots, testing workflows, release automation label Jun 2, 2026
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the only one that's failing: pydata/xarray/actions/runs/26844047852/job/79159106197?pr=11370 This shows 59 failing tests, compared to 176 in the latest scheduled run on main: pydata/xarray/actions/runs/26791334945/job/78978472251

I think the reason for that is that numpy is installed through conda and not from the scientific-python nightly wheels repo.

Good catch, thanks for noticing that. It turns out the stubs require a released numpy which bumps numpy off the nightly wheels:

  • scipy-stubs (via optype -> numpy-typing-compat) requires numpy<2.5
  • pandas-stubes requires numpy<=2.3.5
  • types-networkx pulls a conda numpy

It's not possible to have an upstream environment with nightly numpy and typing across the dependency suite. I have therefore split the upstream test run and upstream type checking:

  • test-nightly (the pytest just) stays stub-free and keeps the nightly numpy restoring the failures
  • mypy-upstream (a new env for mypy-upstream-dev) carries the typing toolchain + stubs.

The mypy-upstream uses a released numpy, but I don't see a way around that given the pins.

@keewis

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I was thinking that we'd put all the types-* / *-stubs packages in pypi-packages (since that's what mypy would do to install these, anyways), but indeed it appears that numpy-typing-compat has an upper bound through the version of optype (neither pandas-stubs nor types-networkx appear to have an upper bound on numpy, but installing them through conda will introduce an artificial pin on numpy, and potentially the same with hypothesis)

@maxrjones

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I was thinking that we'd put all the types-* / *-stubs packages in pypi-packages (since that's what mypy would do to install these, anyways), but indeed it appears that numpy-typing-compat has an upper bound through the version of optype (neither pandas-stubs nor types-networkx appear to have an upper bound on numpy, but installing them through conda will introduce an artificial pin on numpy, and potentially the same with hypothesis)

yes, it's messy 😞 Are you alright with the current approach in this PR (not having numpy nightly in the mypy checks)?

@keewis

keewis commented Jun 3, 2026

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I'm fine with it personally so I'll go ahead and merge. I've opened #11371 to keep track of the issue.

@keewis
keewis merged commit d93d0ab into pydata:mainJun 3, 2026
42 of 43 checks passed
sdiebolt pushed a commit to sdiebolt/xarray that referenced this pull request Aug 12, 2026
* ci: move pandas/scipy stubs to pypi deps so typing works in test-nightly
* ci: confine pypi stubs to nightly env
* ci: type-check the dev stack in a dedicated mypy-upstream env
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms"); } } catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
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ci: move pandas/scipy stubs to pypi deps - #11370

Merged
keewis merged 3 commits into
pydata:mainfrom
maxrjones:fix/mypy-type-envs
Jun 3, 2026
Merged

ci: move pandas/scipy stubs to pypi deps#11370
keewis merged 3 commits into
pydata:mainfrom
maxrjones:fix/mypy-type-envs

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@maxrjones

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Description

This PR moves the pandas/scipy stubs to pypi deps so that the test-nightly workflow succeeds, as discussed in #11279. With the previous version, mypy in test-nightly floated to >2 and lacked pip in the env , which caused a lot of failures.

Checklist

  • Closes #xxxx
  • Tests added
  • User visible changes (including notable bug fixes) are documented in whats-new.rst
  • New functions/methods are listed in api.rst

AI Disclosure

  • This PR contains AI-generated content.
    • I have tested any AI-generated content in my PR.
    • I take responsibility for any AI-generated content in my PR. Tools: {e.g., Claude, Codex, GitHub Copilot, ChatGPT, etc.}

@keewiskeewis added the run-upstream Run upstream CI label Jun 2, 2026
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cc @Illviljan

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looks good to me, but why does this resolve >100 tests that are failing on main?

@maxrjones

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why does this resolve >100 tests that are failing on main?

Which workflow are you looking at?

@keewis

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the only one that's failing: https://github.com/pydata/xarray/actions/runs/26844047852/job/79159106197?pr=11370 This shows 59 failing tests, compared to 176 in the latest scheduled run on main: https://github.com/pydata/xarray/actions/runs/26791334945/job/78978472251

I think the reason for that is that numpy is installed through conda and not from the scientific-python nightly wheels repo.

@github-actionsgithub-actionsBot added the Automation Github bots, testing workflows, release automation label Jun 2, 2026
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the only one that's failing: pydata/xarray/actions/runs/26844047852/job/79159106197?pr=11370 This shows 59 failing tests, compared to 176 in the latest scheduled run on main: pydata/xarray/actions/runs/26791334945/job/78978472251

I think the reason for that is that numpy is installed through conda and not from the scientific-python nightly wheels repo.

Good catch, thanks for noticing that. It turns out the stubs require a released numpy which bumps numpy off the nightly wheels:

  • scipy-stubs (via optype -> numpy-typing-compat) requires numpy<2.5
  • pandas-stubes requires numpy<=2.3.5
  • types-networkx pulls a conda numpy

It's not possible to have an upstream environment with nightly numpy and typing across the dependency suite. I have therefore split the upstream test run and upstream type checking:

  • test-nightly (the pytest just) stays stub-free and keeps the nightly numpy restoring the failures
  • mypy-upstream (a new env for mypy-upstream-dev) carries the typing toolchain + stubs.

The mypy-upstream uses a released numpy, but I don't see a way around that given the pins.

@keewis

Copy link
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I was thinking that we'd put all the types-* / *-stubs packages in pypi-packages (since that's what mypy would do to install these, anyways), but indeed it appears that numpy-typing-compat has an upper bound through the version of optype (neither pandas-stubs nor types-networkx appear to have an upper bound on numpy, but installing them through conda will introduce an artificial pin on numpy, and potentially the same with hypothesis)

@maxrjones

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I was thinking that we'd put all the types-* / *-stubs packages in pypi-packages (since that's what mypy would do to install these, anyways), but indeed it appears that numpy-typing-compat has an upper bound through the version of optype (neither pandas-stubs nor types-networkx appear to have an upper bound on numpy, but installing them through conda will introduce an artificial pin on numpy, and potentially the same with hypothesis)

yes, it's messy 😞 Are you alright with the current approach in this PR (not having numpy nightly in the mypy checks)?

@keewis

keewis commented Jun 3, 2026

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I'm fine with it personally so I'll go ahead and merge. I've opened #11371 to keep track of the issue.

@keewis
keewis merged commit d93d0ab into pydata:mainJun 3, 2026
42 of 43 checks passed
sdiebolt pushed a commit to sdiebolt/xarray that referenced this pull request Aug 12, 2026
* ci: move pandas/scipy stubs to pypi deps so typing works in test-nightly
* ci: confine pypi stubs to nightly env
* ci: type-check the dev stack in a dedicated mypy-upstream env
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ci: move pandas/scipy stubs to pypi deps - #11370

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keewis merged 3 commits into
pydata:mainfrom
maxrjones:fix/mypy-type-envs
Jun 3, 2026
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ci: move pandas/scipy stubs to pypi deps#11370
keewis merged 3 commits into
pydata:mainfrom
maxrjones:fix/mypy-type-envs

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Description

This PR moves the pandas/scipy stubs to pypi deps so that the test-nightly workflow succeeds, as discussed in #11279. With the previous version, mypy in test-nightly floated to >2 and lacked pip in the env , which caused a lot of failures.

Checklist

  • Closes #xxxx
  • Tests added
  • User visible changes (including notable bug fixes) are documented in whats-new.rst
  • New functions/methods are listed in api.rst

AI Disclosure

  • This PR contains AI-generated content.
    • I have tested any AI-generated content in my PR.
    • I take responsibility for any AI-generated content in my PR. Tools: {e.g., Claude, Codex, GitHub Copilot, ChatGPT, etc.}

@keewiskeewis added the run-upstream Run upstream CI label Jun 2, 2026
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cc @Illviljan

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looks good to me, but why does this resolve >100 tests that are failing on main?

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why does this resolve >100 tests that are failing on main?

Which workflow are you looking at?

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the only one that's failing: https://github.com/pydata/xarray/actions/runs/26844047852/job/79159106197?pr=11370 This shows 59 failing tests, compared to 176 in the latest scheduled run on main: https://github.com/pydata/xarray/actions/runs/26791334945/job/78978472251

I think the reason for that is that numpy is installed through conda and not from the scientific-python nightly wheels repo.

@github-actionsgithub-actionsBot added the Automation Github bots, testing workflows, release automation label Jun 2, 2026
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the only one that's failing: pydata/xarray/actions/runs/26844047852/job/79159106197?pr=11370 This shows 59 failing tests, compared to 176 in the latest scheduled run on main: pydata/xarray/actions/runs/26791334945/job/78978472251

I think the reason for that is that numpy is installed through conda and not from the scientific-python nightly wheels repo.

Good catch, thanks for noticing that. It turns out the stubs require a released numpy which bumps numpy off the nightly wheels:

  • scipy-stubs (via optype -> numpy-typing-compat) requires numpy<2.5
  • pandas-stubes requires numpy<=2.3.5
  • types-networkx pulls a conda numpy

It's not possible to have an upstream environment with nightly numpy and typing across the dependency suite. I have therefore split the upstream test run and upstream type checking:

  • test-nightly (the pytest just) stays stub-free and keeps the nightly numpy restoring the failures
  • mypy-upstream (a new env for mypy-upstream-dev) carries the typing toolchain + stubs.

The mypy-upstream uses a released numpy, but I don't see a way around that given the pins.

@keewis

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I was thinking that we'd put all the types-* / *-stubs packages in pypi-packages (since that's what mypy would do to install these, anyways), but indeed it appears that numpy-typing-compat has an upper bound through the version of optype (neither pandas-stubs nor types-networkx appear to have an upper bound on numpy, but installing them through conda will introduce an artificial pin on numpy, and potentially the same with hypothesis)

@maxrjones

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I was thinking that we'd put all the types-* / *-stubs packages in pypi-packages (since that's what mypy would do to install these, anyways), but indeed it appears that numpy-typing-compat has an upper bound through the version of optype (neither pandas-stubs nor types-networkx appear to have an upper bound on numpy, but installing them through conda will introduce an artificial pin on numpy, and potentially the same with hypothesis)

yes, it's messy 😞 Are you alright with the current approach in this PR (not having numpy nightly in the mypy checks)?

@keewis

keewis commented Jun 3, 2026

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I'm fine with it personally so I'll go ahead and merge. I've opened #11371 to keep track of the issue.

@keewis
keewis merged commit d93d0ab into pydata:mainJun 3, 2026
42 of 43 checks passed
sdiebolt pushed a commit to sdiebolt/xarray that referenced this pull request Aug 12, 2026
* ci: move pandas/scipy stubs to pypi deps so typing works in test-nightly
* ci: confine pypi stubs to nightly env
* ci: type-check the dev stack in a dedicated mypy-upstream env
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default"); } } catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
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ci: move pandas/scipy stubs to pypi deps - #11370

Merged
keewis merged 3 commits into
pydata:mainfrom
maxrjones:fix/mypy-type-envs
Jun 3, 2026
Merged

ci: move pandas/scipy stubs to pypi deps#11370
keewis merged 3 commits into
pydata:mainfrom
maxrjones:fix/mypy-type-envs

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@maxrjones

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Description

This PR moves the pandas/scipy stubs to pypi deps so that the test-nightly workflow succeeds, as discussed in #11279. With the previous version, mypy in test-nightly floated to >2 and lacked pip in the env , which caused a lot of failures.

Checklist

  • Closes #xxxx
  • Tests added
  • User visible changes (including notable bug fixes) are documented in whats-new.rst
  • New functions/methods are listed in api.rst

AI Disclosure

  • This PR contains AI-generated content.
    • I have tested any AI-generated content in my PR.
    • I take responsibility for any AI-generated content in my PR. Tools: {e.g., Claude, Codex, GitHub Copilot, ChatGPT, etc.}

@keewiskeewis added the run-upstream Run upstream CI label Jun 2, 2026
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cc @Illviljan

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looks good to me, but why does this resolve >100 tests that are failing on main?

@maxrjones

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why does this resolve >100 tests that are failing on main?

Which workflow are you looking at?

@keewis

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the only one that's failing: https://github.com/pydata/xarray/actions/runs/26844047852/job/79159106197?pr=11370 This shows 59 failing tests, compared to 176 in the latest scheduled run on main: https://github.com/pydata/xarray/actions/runs/26791334945/job/78978472251

I think the reason for that is that numpy is installed through conda and not from the scientific-python nightly wheels repo.

@github-actionsgithub-actionsBot added the Automation Github bots, testing workflows, release automation label Jun 2, 2026
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the only one that's failing: pydata/xarray/actions/runs/26844047852/job/79159106197?pr=11370 This shows 59 failing tests, compared to 176 in the latest scheduled run on main: pydata/xarray/actions/runs/26791334945/job/78978472251

I think the reason for that is that numpy is installed through conda and not from the scientific-python nightly wheels repo.

Good catch, thanks for noticing that. It turns out the stubs require a released numpy which bumps numpy off the nightly wheels:

  • scipy-stubs (via optype -> numpy-typing-compat) requires numpy<2.5
  • pandas-stubes requires numpy<=2.3.5
  • types-networkx pulls a conda numpy

It's not possible to have an upstream environment with nightly numpy and typing across the dependency suite. I have therefore split the upstream test run and upstream type checking:

  • test-nightly (the pytest just) stays stub-free and keeps the nightly numpy restoring the failures
  • mypy-upstream (a new env for mypy-upstream-dev) carries the typing toolchain + stubs.

The mypy-upstream uses a released numpy, but I don't see a way around that given the pins.

@keewis

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I was thinking that we'd put all the types-* / *-stubs packages in pypi-packages (since that's what mypy would do to install these, anyways), but indeed it appears that numpy-typing-compat has an upper bound through the version of optype (neither pandas-stubs nor types-networkx appear to have an upper bound on numpy, but installing them through conda will introduce an artificial pin on numpy, and potentially the same with hypothesis)

@maxrjones

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I was thinking that we'd put all the types-* / *-stubs packages in pypi-packages (since that's what mypy would do to install these, anyways), but indeed it appears that numpy-typing-compat has an upper bound through the version of optype (neither pandas-stubs nor types-networkx appear to have an upper bound on numpy, but installing them through conda will introduce an artificial pin on numpy, and potentially the same with hypothesis)

yes, it's messy 😞 Are you alright with the current approach in this PR (not having numpy nightly in the mypy checks)?

@keewis

keewis commented Jun 3, 2026

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I'm fine with it personally so I'll go ahead and merge. I've opened #11371 to keep track of the issue.

@keewis
keewis merged commit d93d0ab into pydata:mainJun 3, 2026
42 of 43 checks passed
sdiebolt pushed a commit to sdiebolt/xarray that referenced this pull request Aug 12, 2026
* ci: move pandas/scipy stubs to pypi deps so typing works in test-nightly
* ci: confine pypi stubs to nightly env
* ci: type-check the dev stack in a dedicated mypy-upstream env
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers"); } } catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
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ci: move pandas/scipy stubs to pypi deps - #11370

Merged
keewis merged 3 commits into
pydata:mainfrom
maxrjones:fix/mypy-type-envs
Jun 3, 2026
Merged

ci: move pandas/scipy stubs to pypi deps#11370
keewis merged 3 commits into
pydata:mainfrom
maxrjones:fix/mypy-type-envs

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@maxrjones

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Description

This PR moves the pandas/scipy stubs to pypi deps so that the test-nightly workflow succeeds, as discussed in #11279. With the previous version, mypy in test-nightly floated to >2 and lacked pip in the env , which caused a lot of failures.

Checklist

  • Closes #xxxx
  • Tests added
  • User visible changes (including notable bug fixes) are documented in whats-new.rst
  • New functions/methods are listed in api.rst

AI Disclosure

  • This PR contains AI-generated content.
    • I have tested any AI-generated content in my PR.
    • I take responsibility for any AI-generated content in my PR. Tools: {e.g., Claude, Codex, GitHub Copilot, ChatGPT, etc.}

@keewiskeewis added the run-upstream Run upstream CI label Jun 2, 2026
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cc @Illviljan

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looks good to me, but why does this resolve >100 tests that are failing on main?

@maxrjones

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why does this resolve >100 tests that are failing on main?

Which workflow are you looking at?

@keewis

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the only one that's failing: https://github.com/pydata/xarray/actions/runs/26844047852/job/79159106197?pr=11370 This shows 59 failing tests, compared to 176 in the latest scheduled run on main: https://github.com/pydata/xarray/actions/runs/26791334945/job/78978472251

I think the reason for that is that numpy is installed through conda and not from the scientific-python nightly wheels repo.

@github-actionsgithub-actionsBot added the Automation Github bots, testing workflows, release automation label Jun 2, 2026
@maxrjones

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the only one that's failing: pydata/xarray/actions/runs/26844047852/job/79159106197?pr=11370 This shows 59 failing tests, compared to 176 in the latest scheduled run on main: pydata/xarray/actions/runs/26791334945/job/78978472251

I think the reason for that is that numpy is installed through conda and not from the scientific-python nightly wheels repo.

Good catch, thanks for noticing that. It turns out the stubs require a released numpy which bumps numpy off the nightly wheels:

  • scipy-stubs (via optype -> numpy-typing-compat) requires numpy<2.5
  • pandas-stubes requires numpy<=2.3.5
  • types-networkx pulls a conda numpy

It's not possible to have an upstream environment with nightly numpy and typing across the dependency suite. I have therefore split the upstream test run and upstream type checking:

  • test-nightly (the pytest just) stays stub-free and keeps the nightly numpy restoring the failures
  • mypy-upstream (a new env for mypy-upstream-dev) carries the typing toolchain + stubs.

The mypy-upstream uses a released numpy, but I don't see a way around that given the pins.

@keewis

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I was thinking that we'd put all the types-* / *-stubs packages in pypi-packages (since that's what mypy would do to install these, anyways), but indeed it appears that numpy-typing-compat has an upper bound through the version of optype (neither pandas-stubs nor types-networkx appear to have an upper bound on numpy, but installing them through conda will introduce an artificial pin on numpy, and potentially the same with hypothesis)

@maxrjones

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I was thinking that we'd put all the types-* / *-stubs packages in pypi-packages (since that's what mypy would do to install these, anyways), but indeed it appears that numpy-typing-compat has an upper bound through the version of optype (neither pandas-stubs nor types-networkx appear to have an upper bound on numpy, but installing them through conda will introduce an artificial pin on numpy, and potentially the same with hypothesis)

yes, it's messy 😞 Are you alright with the current approach in this PR (not having numpy nightly in the mypy checks)?

@keewis

keewis commented Jun 3, 2026

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I'm fine with it personally so I'll go ahead and merge. I've opened #11371 to keep track of the issue.

@keewis
keewis merged commit d93d0ab into pydata:mainJun 3, 2026
42 of 43 checks passed
sdiebolt pushed a commit to sdiebolt/xarray that referenced this pull request Aug 12, 2026
* ci: move pandas/scipy stubs to pypi deps so typing works in test-nightly
* ci: confine pypi stubs to nightly env
* ci: type-check the dev stack in a dedicated mypy-upstream env
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode"); } } catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); } })(); })();
Skip to content

ci: move pandas/scipy stubs to pypi deps - #11370

Merged
keewis merged 3 commits into
pydata:mainfrom
maxrjones:fix/mypy-type-envs
Jun 3, 2026
Merged

ci: move pandas/scipy stubs to pypi deps#11370
keewis merged 3 commits into
pydata:mainfrom
maxrjones:fix/mypy-type-envs

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@maxrjones

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Description

This PR moves the pandas/scipy stubs to pypi deps so that the test-nightly workflow succeeds, as discussed in #11279. With the previous version, mypy in test-nightly floated to >2 and lacked pip in the env , which caused a lot of failures.

Checklist

  • Closes #xxxx
  • Tests added
  • User visible changes (including notable bug fixes) are documented in whats-new.rst
  • New functions/methods are listed in api.rst

AI Disclosure

  • This PR contains AI-generated content.
    • I have tested any AI-generated content in my PR.
    • I take responsibility for any AI-generated content in my PR. Tools: {e.g., Claude, Codex, GitHub Copilot, ChatGPT, etc.}

@keewiskeewis added the run-upstream Run upstream CI label Jun 2, 2026
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cc @Illviljan

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looks good to me, but why does this resolve >100 tests that are failing on main?

@maxrjones

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why does this resolve >100 tests that are failing on main?

Which workflow are you looking at?

@keewis

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the only one that's failing: https://github.com/pydata/xarray/actions/runs/26844047852/job/79159106197?pr=11370 This shows 59 failing tests, compared to 176 in the latest scheduled run on main: https://github.com/pydata/xarray/actions/runs/26791334945/job/78978472251

I think the reason for that is that numpy is installed through conda and not from the scientific-python nightly wheels repo.

@github-actionsgithub-actionsBot added the Automation Github bots, testing workflows, release automation label Jun 2, 2026
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the only one that's failing: pydata/xarray/actions/runs/26844047852/job/79159106197?pr=11370 This shows 59 failing tests, compared to 176 in the latest scheduled run on main: pydata/xarray/actions/runs/26791334945/job/78978472251

I think the reason for that is that numpy is installed through conda and not from the scientific-python nightly wheels repo.

Good catch, thanks for noticing that. It turns out the stubs require a released numpy which bumps numpy off the nightly wheels:

  • scipy-stubs (via optype -> numpy-typing-compat) requires numpy<2.5
  • pandas-stubes requires numpy<=2.3.5
  • types-networkx pulls a conda numpy

It's not possible to have an upstream environment with nightly numpy and typing across the dependency suite. I have therefore split the upstream test run and upstream type checking:

  • test-nightly (the pytest just) stays stub-free and keeps the nightly numpy restoring the failures
  • mypy-upstream (a new env for mypy-upstream-dev) carries the typing toolchain + stubs.

The mypy-upstream uses a released numpy, but I don't see a way around that given the pins.

@keewis

Copy link
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I was thinking that we'd put all the types-* / *-stubs packages in pypi-packages (since that's what mypy would do to install these, anyways), but indeed it appears that numpy-typing-compat has an upper bound through the version of optype (neither pandas-stubs nor types-networkx appear to have an upper bound on numpy, but installing them through conda will introduce an artificial pin on numpy, and potentially the same with hypothesis)

@maxrjones

Copy link
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ContributorAuthor

I was thinking that we'd put all the types-* / *-stubs packages in pypi-packages (since that's what mypy would do to install these, anyways), but indeed it appears that numpy-typing-compat has an upper bound through the version of optype (neither pandas-stubs nor types-networkx appear to have an upper bound on numpy, but installing them through conda will introduce an artificial pin on numpy, and potentially the same with hypothesis)

yes, it's messy 😞 Are you alright with the current approach in this PR (not having numpy nightly in the mypy checks)?

@keewis

keewis commented Jun 3, 2026

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I'm fine with it personally so I'll go ahead and merge. I've opened #11371 to keep track of the issue.

@keewis
keewis merged commit d93d0ab into pydata:mainJun 3, 2026
42 of 43 checks passed
sdiebolt pushed a commit to sdiebolt/xarray that referenced this pull request Aug 12, 2026
* ci: move pandas/scipy stubs to pypi deps so typing works in test-nightly
* ci: confine pypi stubs to nightly env
* ci: type-check the dev stack in a dedicated mypy-upstream env
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