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SBC-Utrecht / pytom-match-pick

GPU-accelerated template matching for cryo-ET
https://sbc-utrecht.github.io/pytom-match-pick/
GNU General Public License v2.0
29 stars 9 forks source link

[DO NOT MERGE] debug pypi workflow #241

Closed sroet closed 1 week ago

sroet commented 1 week ago

@webknjaz, current results from running the ls commands inside the container: ls /home returns nothing ls /__w/_actions returns

actions
pypa

anything else you want me to check?

webknjaz commented 1 week ago

But what about the subdirs? ls - R should show that

github-actions[bot] commented 1 week ago

File Coverage Missing
All files 89% :white_check_mark:
src/pytom_tm/correlation.py 85% :x: 97-98 130
src/pytom_tm/entry_points.py 80% :x: 30 115-132 237-282 387-406 559-579 1092-1103
src/pytom_tm/extract.py 97% :white_check_mark: 264-269
src/pytom_tm/io.py 84% :x: 20 40 56 72 85 104-110 127-131 138 144 181 186 233-235 305 451-459 484
src/pytom_tm/mask.py 80% :x: 75 93 103-104
src/pytom_tm/parallel.py 89% :white_check_mark: 14-15 93 104-105 111 176
src/pytom_tm/plotting.py 16% :x: 19-21 24-31 35-43 47-50 53-69 72-73 76-77 97-102 118-126 132-149 164-172 176-193 197-205 209-216 222 228 233 247-397
src/pytom_tm/tmjob.py 98% :white_check_mark: 371-372 388 482 610 659
src/pytom_tm/utils.py 78% :x: 18-20
src/pytom_tm/weights.py 96% :white_check_mark: 58 313-317 324 534 539 544

Minimum allowed coverage is 88%

Generated by :monkey: cobertura-action against 99de9f8217f54d7b57484689532dfd0271a39ba9

sroet commented 1 week ago

this run runs ls / and ls -R /__w/ let me know if you want me to run ls -R / (wanted to keep the output somewhat relevant)

ls /

__e
__w
bin
boot
dev
etc
github
home
lib
lib64
media
mnt
opt
proc
root
run
sbin
srv
sys
tmp
usr
var
ls -R /__w/

/__w/:
_PipelineMapping
_actions
_temp
_tool
_update
_update.sh
pytom-match-pick
pytom-template-matching-gpu
/__w/_PipelineMapping:
SBC-Utrecht
/__w/_PipelineMapping/SBC-Utrecht:
pytom-match-pick
pytom-template-matching-gpu
/__w/_PipelineMapping/SBC-Utrecht/pytom-match-pick:
PipelineFolder.json
/__w/_PipelineMapping/SBC-Utrecht/pytom-template-matching-gpu:
PipelineFolder.json
/__w/_actions:
actions
pypa
/__w/_actions/actions:
checkout
setup-python
/__w/_actions/actions/checkout:
v4
v4.completed
/__w/_actions/actions/checkout/v4:
CHANGELOG.md
CODEOWNERS
CONTRIBUTING.md
LICENSE
README.md
__test__
action.yml
adrs
dist
images
jest.config.js
package-lock.json
package.json
src
tsconfig.json
/__w/_actions/actions/checkout/v4/__test__:
git-auth-helper.test.ts
git-command-manager.test.ts
git-directory-helper.test.ts
git-version.test.ts
input-helper.test.ts
modify-work-tree.sh
override-git-version.cmd
override-git-version.sh
ref-helper.test.ts
retry-helper.test.ts
url-helper.test.ts
verify-basic.sh
verify-clean.sh
verify-fetch-filter.sh
verify-lfs.sh
verify-no-unstaged-changes.sh
verify-side-by-side.sh
verify-sparse-checkout-non-cone-mode.sh
verify-sparse-checkout.sh
verify-submodules-false.sh
verify-submodules-recursive.sh
verify-submodules-true.sh
/__w/_actions/actions/checkout/v4/adrs:
0153-checkout-v2.md
/__w/_actions/actions/checkout/v4/dist:
index.js
problem-matcher.json
/__w/_actions/actions/checkout/v4/images:
test-ubuntu-git.Dockerfile
test-ubuntu-git.md
/__w/_actions/actions/checkout/v4/src:
fs-helper.ts
git-auth-helper.ts
git-command-manager.ts
git-directory-helper.ts
git-source-provider.ts
git-source-settings.ts
git-version.ts
github-api-helper.ts
input-helper.ts
main.ts
misc
ref-helper.ts
regexp-helper.ts
retry-helper.ts
state-helper.ts
url-helper.ts
workflow-context-helper.ts
/__w/_actions/actions/checkout/v4/src/misc:
generate-docs.ts
licensed-check.sh
licensed-download.sh
licensed-generate.sh
/__w/_actions/actions/setup-python:
v5
v5.completed
/__w/_actions/actions/setup-python/v5:
CODE_OF_CONDUCT.md
LICENSE
README.md
__tests__
action.yml
dist
docs
jest.config.js
package-lock.json
package.json
src
tsconfig.json
/__w/_actions/actions/setup-python/v5/__tests__:
cache-restore.test.ts
cache-save.test.ts
check-python-path.sh
data
find-graalpy.test.ts
find-pypy.test.ts
finder.test.ts
install-graalpy.test.ts
install-pypy.test.ts
install-python.test.ts
test-pipenv.py
utils.test.ts
verify-python.py
/__w/_actions/actions/setup-python/v5/__tests__/data:
Pipfile
Pipfile.lock
graalpy.json
inner
pipenv-requirements.txt
poetry.lock
pyproject.toml
pypy.json
requirements-linux.txt
requirements.txt
versions-manifest.json
/__w/_actions/actions/setup-python/v5/__tests__/data/inner:
poetry.lock
pyproject.toml
/__w/_actions/actions/setup-python/v5/dist:
cache-save
setup
/__w/_actions/actions/setup-python/v5/dist/cache-save:
index.js
/__w/_actions/actions/setup-python/v5/dist/setup:
index.js
/__w/_actions/actions/setup-python/v5/docs:
adrs
advanced-usage.md
contributors.md
/__w/_actions/actions/setup-python/v5/docs/adrs:
0000-caching-dependencies.md
/__w/_actions/actions/setup-python/v5/src:
cache-distributions
cache-save.ts
find-graalpy.ts
find-pypy.ts
find-python.ts
install-graalpy.ts
install-pypy.ts
install-python.ts
setup-python.ts
utils.ts
/__w/_actions/actions/setup-python/v5/src/cache-distributions:
cache-distributor.ts
cache-factory.ts
constants.ts
pip-cache.ts
pipenv-cache.ts
poetry-cache.ts
/__w/_actions/pypa:
gh-action-pypi-publish
/__w/_actions/pypa/gh-action-pypi-publish:
release
/__w/_actions/pypa/gh-action-pypi-publish/release:
v1
v1.completed
/__w/_actions/pypa/gh-action-pypi-publish/release/v1:
Dockerfile
LICENSE.md
README.md
action.yml
attestations.py
create-docker-action.py
oidc-exchange.py
print-hash.py
print-pkg-names.py
requirements
twine-upload.sh
/__w/_actions/pypa/gh-action-pypi-publish/release/v1/requirements:
runtime-prerequisites.in
runtime-prerequisites.txt
runtime.in
runtime.txt
/__w/_temp:
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997ae293-979c-439e-b9bf-582635e11879.sh
_github_home
_github_workflow
_runner_file_commands
a1f972b8-0a1b-434c-a6e6-740ccbd738c0.sh
abb619ef-9667-4f4d-8133-4a3efb5f45b6.sh
c8e451a4-e73e-4bd5-ae46-4d65dffabc3e.sh
/__w/_temp/_github_home:
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/__w/_temp/_runner_file_commands:
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add_path_63ea0022-ca5c-4dae-b9d9-bab204a2b7fc
add_path_83008e07-a49a-402b-a877-b1f04c87c531
add_path_8d53c6e0-682e-4abd-b2d5-4453eeca04ce
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set_env_63ea0022-ca5c-4dae-b9d9-bab204a2b7fc
set_env_83008e07-a49a-402b-a877-b1f04c87c531
set_env_8d53c6e0-682e-4abd-b2d5-4453eeca04ce
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set_output_63ea0022-ca5c-4dae-b9d9-bab204a2b7fc
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set_output_8d53c6e0-682e-4abd-b2d5-4453eeca04ce
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step_summary_3ef6bb8d-746a-45ed-99ba-8cb58b160bae
step_summary_5865228f-559c-4e5b-b1a2-f68843ce4a46
step_summary_63ea0022-ca5c-4dae-b9d9-bab204a2b7fc
step_summary_83008e07-a49a-402b-a877-b1f04c87c531
step_summary_8d53c6e0-682e-4abd-b2d5-4453eeca04ce
/__w/_tool:
/__w/_update:
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config.sh
env.sh
externals
run-helper.cmd.template
run-helper.sh.template
run.sh
safe_sleep.sh
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Azure.Storage.Blobs.dll
Azure.Storage.Common.dll
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Runner.Common.deps.json
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Runner.PluginHost.dll
Runner.PluginHost.runtimeconfig.json
Runner.Plugins.deps.json
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Runner.Sdk.deps.json
Runner.Sdk.dll
Runner.Worker
Runner.Worker.deps.json
Runner.Worker.dll
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Sdk.dll
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System.Buffers.dll
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System.Configuration.dll
System.Console.dll
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System.Data.Common.dll
System.Data.DataSetExtensions.dll
System.Data.dll
System.Diagnostics.Contracts.dll
System.Diagnostics.Debug.dll
System.Diagnostics.DiagnosticSource.dll
System.Diagnostics.FileVersionInfo.dll
System.Diagnostics.Process.dll
System.Diagnostics.StackTrace.dll
System.Diagnostics.TextWriterTraceListener.dll
System.Diagnostics.Tools.dll
System.Diagnostics.TraceSource.dll
System.Diagnostics.Tracing.dll
System.Drawing.Primitives.dll
System.Drawing.dll
System.Dynamic.Runtime.dll
System.Formats.Asn1.dll
System.Globalization.Calendars.dll
System.Globalization.Extensions.dll
System.Globalization.dll
System.IO.Compression.Brotli.dll
System.IO.Compression.FileSystem.dll
System.IO.Compression.ZipFile.dll
System.IO.Compression.dll
System.IO.FileSystem.AccessControl.dll
System.IO.FileSystem.DriveInfo.dll
System.IO.FileSystem.Primitives.dll
System.IO.FileSystem.Watcher.dll
System.IO.FileSystem.dll
System.IO.Hashing.dll
System.IO.IsolatedStorage.dll
System.IO.MemoryMappedFiles.dll
System.IO.Pipes.AccessControl.dll
System.IO.Pipes.dll
System.IO.UnmanagedMemoryStream.dll
System.IO.dll
System.IdentityModel.Tokens.Jwt.dll
System.Linq.Expressions.dll
System.Linq.Parallel.dll
System.Linq.Queryable.dll
System.Linq.dll
System.Memory.Data.dll
System.Memory.dll
System.Net.Http.Formatting.dll
System.Net.Http.Json.dll
System.Net.Http.dll
System.Net.HttpListener.dll
System.Net.Mail.dll
System.Net.NameResolution.dll
System.Net.NetworkInformation.dll
System.Net.Ping.dll
System.Net.Primitives.dll
System.Net.Quic.dll
System.Net.Requests.dll
System.Net.Security.dll
System.Net.ServicePoint.dll
System.Net.Sockets.dll
System.Net.WebClient.dll
System.Net.WebHeaderCollection.dll
System.Net.WebProxy.dll
System.Net.WebSockets.Client.dll
System.Net.WebSockets.dll
System.Net.dll
System.Numerics.Vectors.dll
System.Numerics.dll
System.ObjectModel.dll
System.Private.CoreLib.dll
System.Private.DataContractSerialization.dll
System.Private.Uri.dll
System.Private.Xml.Linq.dll
System.Private.Xml.dll
System.Reflection.DispatchProxy.dll
System.Reflection.Emit.ILGeneration.dll
System.Reflection.Emit.Lightweight.dll
System.Reflection.Emit.dll
System.Reflection.Extensions.dll
System.Reflection.Metadata.dll
System.Reflection.Primitives.dll
System.Reflection.TypeExtensions.dll
System.Reflection.dll
System.Resources.Reader.dll
System.Resources.ResourceManager.dll
System.Resources.Writer.dll
System.Runtime.CompilerServices.Unsafe.dll
System.Runtime.CompilerServices.VisualC.dll
System.Runtime.Extensions.dll
System.Runtime.Handles.dll
System.Runtime.InteropServices.RuntimeInformation.dll
System.Runtime.InteropServices.dll
System.Runtime.Intrinsics.dll
System.Runtime.Loader.dll
System.Runtime.Numerics.dll
System.Runtime.Serialization.Formatters.dll
System.Runtime.Serialization.Json.dll
System.Runtime.Serialization.Primitives.dll
System.Runtime.Serialization.Xml.dll
System.Runtime.Serialization.dll
System.Runtime.dll
System.Security.AccessControl.dll
System.Security.Claims.dll
System.Security.Cryptography.Algorithms.dll
System.Security.Cryptography.Cng.dll
System.Security.Cryptography.Csp.dll
System.Security.Cryptography.Encoding.dll
System.Security.Cryptography.OpenSsl.dll
System.Security.Cryptography.Pkcs.dll
System.Security.Cryptography.Primitives.dll
System.Security.Cryptography.ProtectedData.dll
System.Security.Cryptography.X509Certificates.dll
System.Security.Principal.Windows.dll
System.Security.Principal.dll
System.Security.SecureString.dll
System.Security.dll
System.ServiceModel.Web.dll
System.ServiceProcess.ServiceController.dll
System.ServiceProcess.dll
System.Text.Encoding.CodePages.dll
System.Text.Encoding.Extensions.dll
System.Text.Encoding.dll
System.Text.Encodings.Web.dll
System.Text.Json.dll
System.Text.RegularExpressions.dll
System.Threading.Channels.dll
System.Threading.Overlapped.dll
System.Threading.Tasks.Dataflow.dll
System.Threading.Tasks.Extensions.dll
System.Threading.Tasks.Parallel.dll
System.Threading.Tasks.dll
System.Threading.Thread.dll
System.Threading.ThreadPool.dll
System.Threading.Timer.dll
System.Threading.dll
System.Transactions.Local.dll
System.Transactions.dll
System.ValueTuple.dll
System.Web.HttpUtility.dll
System.Web.dll
System.Windows.dll
System.Xml.Linq.dll
System.Xml.ReaderWriter.dll
System.Xml.Serialization.dll
System.Xml.XDocument.dll
System.Xml.XPath.XDocument.dll
System.Xml.XPath.dll
System.Xml.XmlDocument.dll
System.Xml.XmlSerializer.dll
System.Xml.dll
System.dll
WindowsBase.dll
YamlDotNet.dll
actions.runner.plist.template
actions.runner.service.template
checkScripts
createdump
darwin.svc.sh.template
hashFiles
installdependencies.sh
libSystem.Globalization.Native.so
libSystem.IO.Compression.Native.so
libSystem.Native.so
libSystem.Net.Security.Native.so
libSystem.Security.Cryptography.Native.OpenSsl.so
libclrjit.so
libcoreclr.so
libcoreclrtraceptprovider.so
libdbgshim.so
libhostfxr.so
libhostpolicy.so
libmscordaccore.so
libmscordbi.so
macos-run-invoker.js
mscorlib.dll
netstandard.dll
runsvc.sh
systemd.svc.sh.template
testDotNet8Compatibility
update.cmd.template
update.sh.template
/__w/_update/bin/checkScripts:
downloadCert.js
makeWebRequest.js
/__w/_update/bin/hashFiles:
index.js
/__w/_update/bin/testDotNet8Compatibility:
Microsoft.CSharp.dll
Microsoft.VisualBasic.Core.dll
Microsoft.VisualBasic.dll
Microsoft.Win32.Primitives.dll
Microsoft.Win32.Registry.dll
System.AppContext.dll
System.Buffers.dll
System.Collections.Concurrent.dll
System.Collections.Immutable.dll
System.Collections.NonGeneric.dll
System.Collections.Specialized.dll
System.Collections.dll
System.ComponentModel.Annotations.dll
System.ComponentModel.DataAnnotations.dll
System.ComponentModel.EventBasedAsync.dll
System.ComponentModel.Primitives.dll
System.ComponentModel.TypeConverter.dll
System.ComponentModel.dll
System.Configuration.dll
System.Console.dll
System.Core.dll
System.Data.Common.dll
System.Data.DataSetExtensions.dll
System.Data.dll
System.Diagnostics.Contracts.dll
System.Diagnostics.Debug.dll
System.Diagnostics.DiagnosticSource.dll
System.Diagnostics.FileVersionInfo.dll
System.Diagnostics.Process.dll
System.Diagnostics.StackTrace.dll
System.Diagnostics.TextWriterTraceListener.dll
System.Diagnostics.Tools.dll
System.Diagnostics.TraceSource.dll
System.Diagnostics.Tracing.dll
System.Drawing.Primitives.dll
System.Drawing.dll
System.Dynamic.Runtime.dll
System.Formats.Asn1.dll
System.Formats.Tar.dll
System.Globalization.Calendars.dll
System.Globalization.Extensions.dll
System.Globalization.dll
System.IO.Compression.Brotli.dll
System.IO.Compression.FileSystem.dll
System.IO.Compression.ZipFile.dll
System.IO.Compression.dll
System.IO.FileSystem.AccessControl.dll
System.IO.FileSystem.DriveInfo.dll
System.IO.FileSystem.Primitives.dll
System.IO.FileSystem.Watcher.dll
System.IO.FileSystem.dll
System.IO.IsolatedStorage.dll
System.IO.MemoryMappedFiles.dll
System.IO.Pipes.AccessControl.dll
System.IO.Pipes.dll
System.IO.UnmanagedMemoryStream.dll
System.IO.dll
System.Linq.Expressions.dll
System.Linq.Parallel.dll
System.Linq.Queryable.dll
System.Linq.dll
System.Memory.dll
System.Net.Http.Json.dll
System.Net.Http.dll
System.Net.HttpListener.dll
System.Net.Mail.dll
System.Net.NameResolution.dll
System.Net.NetworkInformation.dll
System.Net.Ping.dll
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System.Net.WebSockets.Client.dll
System.Net.WebSockets.dll
System.Net.dll
System.Numerics.Vectors.dll
System.Numerics.dll
System.ObjectModel.dll
System.Private.CoreLib.dll
System.Private.DataContractSerialization.dll
System.Private.Uri.dll
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System.ValueTuple.dll
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System.Xml.XPath.dll
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System.Xml.dll
System.dll
TestDotNet8Compatibility
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TestDotNet8Compatibility.dll
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libSystem.Security.Cryptography.Native.OpenSsl.so
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libclrjit.so
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/__w/_update/externals:
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node16_alpine
node20
node20_alpine
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include
lib
share
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node
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config.gypi
cppgc
js_native_api.h
js_native_api_types.h
libplatform
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node_api.h
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node_object_wrap.h
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webknjaz commented 1 week ago

Ah, so /__w/_actions/pypa/gh-action-pypi-publish/release/v1/create-docker-action.py exists but the path being accessed is /home/githubrunner/actions-runner/_work/_actions/pypa/gh-action-pypi-publish/release/v1/create-docker-action.py:

/opt/conda/bin/python3: can't open file '/home/githubrunner/actions-runner/_work/_actions/pypa/gh-action-pypi-publish/release/v1/create-docker-action.py': [Errno 2] No such file or directory

So it seems to me like GitHub Runner does put the host path into the ${{ github.action_path }} variable, and it's then inaccessible within a container. And it's not a problem of our container — this is hit before we get to running it: https://github.com/pypa/gh-action-pypi-publish/blob/93e8795/action.yml#L152C10-L152C61.

The mount point is configured as -v "/home/githubrunner/actions-runner/_work/_actions":"/__w/_actions".

webknjaz commented 1 week ago

So it seems to me like this is a case of a bug in GitHub Runner. And my hunch is that it's probably not caused by it being a hosted runner. It's likely caused by the use of the container setting on the job.

@sroet to verify this, drop the container from the job and try again.

If that's the case, I don't think we'll be attempting to support it (you can probably hack on your container and stick symlinks into it, but that's out of the scope).

Though, I also noticed that you're not following the recommendation of keeping the build invocation out of the job that has elevated OIDC privileges. Perhaps, if you just split it according to https://packaging.python.org/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/, the problem will disappear.

sroet commented 1 week ago

@sroet to verify this, drop the container from the job and try again.

That's not happening as dropping the container from a self-hosted runner will run the code on the actual host machine. Our host machines are not isolated/revertible enough to let random code run on it outside of a container.

Perhaps, if you just split it according to https://packaging.python.org/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/, the problem will disappear.

I can try that, and if that doesn't work maybe push the publishing part to github-runners instead of self-hosted ones

webknjaz commented 1 week ago

maybe push the publishing part to github-runners instead of self-hosted ones

That's exactly what I meant.

sroet commented 1 week ago

So, splitting out the job to run the upload on github runners instead of self-hosted ones seems to work (the failure is expected as this branch can't be valid for the trusted publishing setup we have on this project)

sroet commented 1 week ago

I think all the necessary debugging has been done, so I will close this. @webknjaz thanks for the help and please let me know if you want to test some other things! (Otherwise I will delete this branch in a week)