CI Build & Test: First build incrementally and test changed files only #35652

mkoeppe · 2023-05-19T02:54:27Z

📚 Description

This gives a faster turnaround for errors in the committed changes.
When the incremental build (or the test) fails, we clean thoroughly and build sagelib from scratch (= what happened before this PR.)

Changing the docbuild CI in the same way.

The full doctests are now run with --long.

Also:

Fixes sage -t --new so it works in a git worktree and respects file-level annotations # sage.doctest: optional - ...
Resolves CI doc-build: Include links to changed HTML files #35732

📝 Checklist

The title is concise, informative, and self-explanatory.
The description explains in detail what this PR is about.
I have linked a relevant issue or discussion.
I have created tests covering the changes.
I have updated the documentation accordingly.

⌛ Dependencies

Depends on Add a note on a doctest that randomly behaves #35751 (merged here)

tobiasdiez · 2023-05-25T16:03:52Z

.github/workflows/build.yml

+          git config --global user.email "ci-sage@example.com"
+          git config --global user.name "Build & Test workflow"
+          # If actions/checkout downloaded using the GitHub REST API:
+          if [ ! -d .git ]; then git config --global --add safe.directory $(pwd) && git init && git add -A && git commit --quiet -m "new"; fi


Instead of this git acrobatics, why not get the list of changed files using say https://github.com/marketplace/actions/get-all-changed-files and then run the tests on each of them?

It's not just for finding the changed files.
This trick makes the build of the Sage library actually incremental!

tobiasdiez · 2023-05-25T16:05:58Z

.github/workflows/build.yml

+          eval $(sage-print-system-package-command auto update)
+          eval $(sage-print-system-package-command auto --spkg --yes --no-install-recommends install git)
+
+      - name: Incremental build and test


Why is this coming before the actual build/is this not building things twice now?

We could, in fact, also run the main build on the incrementally updated source tree.

In this "incremental" build, what is build if one changes a python file, a cython file and say something in the build infrastructure (say a package update and a change in setup.py)?

The git acrobatics has exactly the same effect as doing a "git checkout" to the new ref in a full build of the Sage distribution on a developer's computer: The timestamps (mtime) of unmodified files are kept the same, and the timestamps of modified files are newer than any file that was there before.
It is looking so complicated because the source tree in our Docker images is actually not a git working copy. This is why I have to turn it surgically into a working copy (without messing up the timestamps).

Running make build results in an incremental build: For spkgs, if the declared package version is changed, then (because they no longer match the installation records in {local,venv}/var/libs/sage/installed these packages are reinstalled.
For the Sage library, the normal in-tree editable build is run, which is incremental (only the modified Cython files are cythonized and the result compiled). Because we are using editable mode, nothing interesting is happening with the modified Python files.

Thanks for the details!

But doesn't this mean that sometimes the incremental build (+ test) fails? At least locally, I sometimes have to hard-reset everything and run the whole bootstrap + configure + make cycle. In this cases, the workflow would fail, right? I'm not sure if this then more confusing than helpful.

In my experience, incremental builds are very robust, with the following exceptions:

the docbuild process

after indiscriminate updates of system packages (we don't do that here on this workflow)

By "hard reset", do you mean that you do "make distclean" (= remove local and venv)?

Sometimes, but most often I only have to run bootstrap & configure again.

In my experience, incremental builds are very robust, with the following exceptions:

Okay, then I let someone else with more experience on the build process have a look at this PR. Since this is the most important build workflow, it should only fail for the correct reason and not because of some general issues related to the build process.

If the incremental build is not (yet) reliable enough, I would favor a normal build + test on changed files + long test; and/or extracting the incremental build to a new workflow.

By "hard reset", do you mean that you do "make distclean" (= remove local and venv)?

Sometimes, but most often I only have to run bootstrap & configure again.

Ah OK. We can certainly run bootstrap manually before doing the incremental build. I'll make this change.
(configure definitely does not have to be run manually.)

If the incremental build is not (yet) reliable enough, I would favor a normal build + test on changed files + long test; and/or extracting the incremental build to a new workflow.

@tobiasdiez @kwankyu I have now implemented a fallback to non-incremental when the incremental build fails – both for build and for docbuild.

…t changed files

…emental build

kwankyu · 2023-05-27T16:10:50Z

This works well in the step "Incremental build and test", but in the step "Configure new tree" fails with

Run # Reuse built SAGE_LOCAL contained in the Docker image
/__w/_temp/[5](https://github.com/kwankyu/sage/actions/runs/5099185206/jobs/9166745669?pr=23#step:6:6)1d2b[6](https://github.com/kwankyu/sage/actions/runs/5099185206/jobs/9166745669?pr=23#step:6:7)8c-7390-4ae9-a05b-0268b824e3c8.sh: 2: ./configure: not found
Error: Process completed with exit code 127.

and then in the step "Build and test modularized distributions" fails with

...
rc/doc/bootstrap:87: installing src/doc/en/reference/spkg/*.rst
configure.ac:57: installing 'config/compile'
configure.ac:57: installing 'config/config.guess'
configure.ac:57: installing 'config/config.sub'
configure.ac:43: installing 'config/install-sh'
configure.ac:43: installing 'config/missing'
rm -f config.log
mkdir -p logs/pkgs
ln -s logs/pkgs/config.log config.log
****************************************************************************
make[1]: Leaving directory '/__w/sage/sage'
error: Sage source tree is unconfigured. Please run "./configure" first.
note:  Type "./configure --help" to see the available configuration options.
****************************************************************************
make[1]: *** [Makefile:[56](https://github.com/kwankyu/sage/actions/runs/5099185206/jobs/9166745669?pr=23#step:7:57): build/make/Makefile] Error 1
make: *** [Makefile:39: tox] Error 2
Error: Process completed with exit code 2.

…emental build (fixup)

.github/workflows/build.yml

kwankyu · 2023-05-28T02:53:33Z

Thanks.

I am testing it again. So far so good.

Tobias' concern remains. I think incremental build (except doc building) is reliable, but we would not know if it (the concern) is real before we actually deploy incremental build for testing. It is worth to try!

kwankyu · 2023-05-28T09:00:55Z

In my own testing of this PR and also here, we have failure

sage -t --long --random-seed=318874684740931170515189074049952937868 sage/doctest/test.py
**********************************************************************
File "sage/doctest/test.py", line 260, in sage.doctest.test
Failed example:
    os.kill(pid, signal.SIGQUIT) # long time; 10 seconds passed => dead
Expected:
    Traceback (most recent call last):
    ...
    ProcessLookupError: ...
Got:
    <BLANKLINE>
**********************************************************************

kwankyu · 2023-05-28T09:09:55Z

"Build & Test" ran the build workflow of this PR. How is this possible?

mkoeppe · 2023-05-28T15:51:26Z

Strange indeed. I'll restart the workflow to see if this is deterministic

kwankyu · 2023-05-29T00:06:07Z

This seems just normal. GitHub Actions runs workflow on pull_request event in the forked repo, and hence it is safe to run workflows changed in PR?

mkoeppe · 2023-06-12T15:33:35Z

What are dependencies_only files?

See https://doc.sagemath.org/html/en/developer/packaging.html#package-dependencies

I added this when I added dependencies_check files.

kwankyu

Thanks.

mkoeppe · 2023-06-13T00:50:33Z

Thank you!

github-actions · 2023-06-13T01:11:54Z

Documentation preview for this PR (built with commit 908ad71) is ready! 🎉

kwankyu · 2023-06-22T21:11:37Z

Isn't this so designed that if there are doctest failures in the initial incremental build, it is reported and the B&T stops?

mkoeppe · 2023-06-22T21:15:10Z

is it not working as expected?

kwankyu · 2023-06-22T21:33:29Z

See this #35809

kwankyu · 2023-06-22T21:35:59Z

It is not working as I expected. But perhaps it's working as it was designed?

mkoeppe · 2023-06-22T21:36:26Z

In https://github.com/sagemath/sage/actions/runs/5349883585/jobs/9701778982?pr=35809 it is reported by a red X in the step. Are you saying that the final result is a green checkmark but it should be a red X?

kwankyu · 2023-06-22T21:38:12Z

Yes. I expect that the B&T itself stops with red X right after the red X in the step.

kwankyu · 2023-06-22T21:39:30Z

so that people can recognize the failure asap.

kwankyu · 2023-06-22T21:57:15Z

It is okay if it was so designed that the full test always runs. It is an improvement. But It seems a little inconvenient that people need to click the B&T to recognize the doctest failures in the incremental build while the full B&T will take much longer because of --long to get the final result. This is against the whole point of the PR...

mkoeppe · 2023-06-22T22:05:59Z

I did design it so, but you have a very good point.

mkoeppe · 2023-06-22T22:17:44Z

I'll be happy to change this, but I first have to take care of this strange bug:

build.yml: Incremental build&test fails with pytest/matplotlib error #35813

…html    ### 📚 Description This new feature from #35652 was supposed to show the changed HTML files, but a last minute change there destroyed it. Here we fix it.     ### 📝 Checklist  - [x] The title is concise, informative, and self-explanatory. - [ ] The description explains in detail what this PR is about. - [ ] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies   URL: #35808 Reported by: Matthias Köppe Reviewer(s): Kwankyu Lee, Matthias Köppe

### 📚 Description  The CI change in #35652 did not handle the case of a PR that adds files correctly: the fallback to the non-incremental build would delete these files. We fix it here.   Fixes  ### 📝 Checklist  - [x] The title is concise, informative, and self-explanatory. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies   URL: #35865 Reported by: Matthias Köppe Reviewer(s): Dima Pasechnik

Reworking sagemath#35652 as discussed in sagemath#36469 (comment) Also applying the changes made in sagemath#35866 (cosmetic improvements to the Actions logs of doc-build.yml) to doc-build-pdf.yml    ### 📝 Checklist     - [x] The title is concise, informative, and self-explanatory. - [ ] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies   URL: sagemath#36473 Reported by: Matthias Köppe Reviewer(s): Kwankyu Lee, Matthias Köppe

mkoeppe · 2023-11-02T20:24:47Z

It is okay if it was so designed that the full test always runs. It is an improvement. But It seems a little inconvenient that people need to click the B&T to recognize the doctest failures in the incremental build while the full B&T will take much longer because of --long to get the final result. This is against the whole point of the PR...

I'm taking care of this in #36498

@kwankyu

…arate jobs for pyright, build, modularized tests, long tests    Running the containers explicitly, instead of using the declarative `container:` feature of GH Actions gives us more control: - we can create more space on the host if necessary; we just scraped by an out of space condition in sagemath#36473 / sagemath#36469 (comment) - we can run some operations outside of the container but in the same job; this will make the separate "Get CI fixes" jobs unnecessary, addressing the cosmetic concerns from sagemath#36338 (comment), sagemath#36349 - it enables caching between the various workflows (as first discussed in sagemath#36446). We split out static type checking with pyright into its separate workflow: - **pyright.yml**: As static checking does not need a build of the Sage library, for PRs that do not make any changes to packages, there's nothing to build, and the workflow gives a fast turnaround just after 10 minutes. For applying the CI fixes from blocker tickets, this workflow uses the technique favored in sagemath#36349. The workflow **build.yml** first launches a job: - **test-new:** It builds incrementally (using a tox-generated `Dockerfile` and https://github.com/marketplace/actions/build-and-push- docker-images) and does the quick incremental test. This completes within 10 to 20 minutes when there's no change. After this is completed, more jobs are launched: - **test-mod:** It again builds incrementally and tests a modularized distribution. Later (with more from sagemath#35095), more jobs will be added to this matrix job for other distributions. - **test-long:** It again builds incrementally and runs the long test. The workflows **doc-build.yml** and **doc-build-pdf.yml** again build incrementally and then build the documentation. The diffing code for the HTML documentation now runs in the host, not the container, which simplifies things. (To show that diffing still works, we include a small change to the Sage library.) Splitting the workflow jobs implements @kwankyu's suggestion from: - sagemath#35652 (comment) (Fixes sagemath#35814) The steps "again builds incrementally" actually use the GH Actions cache, https://docs.docker.com/build/ci/github-actions/cache/#cache- backend-api. When nothing is cached and the 3 workflows are launched in parallel, they may each build the same thing. But when there's congestion that leads to the workflows to be run serially, the 2nd and 3rd workflow will be able to use the cache from the 1st workflow. This elasticity may be helpful in reducing congestion. There is a rather small per-project limit of 10 GB for this cache, so we'll have to see how effectively caching works in practice. See https://github.com/sagemath/sage/actions/caches   ### 📝 Checklist     - [x] The title is concise, informative, and self-explanatory. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies  - Depends on sagemath#36938 (merged here) - Depends on sagemath#36951 (merged here) - Depends on sagemath#37351 (merged here) - Depends on sagemath#37750 (merged here)  URL: sagemath#36498 Reported by: Matthias Köppe Reviewer(s): Kwankyu Lee, Matthias Köppe

@kwankyu

…arate jobs for pyright, build, modularized tests, long tests    Running the containers explicitly, instead of using the declarative `container:` feature of GH Actions gives us more control: - we can create more space on the host if necessary; we just scraped by an out of space condition in sagemath#36473 / sagemath#36469 (comment) - we can run some operations outside of the container but in the same job; this will make the separate "Get CI fixes" jobs unnecessary, addressing the cosmetic concerns from sagemath#36338 (comment), sagemath#36349 - it enables caching between the various workflows (as first discussed in sagemath#36446). We split out static type checking with pyright into its separate workflow: - **pyright.yml**: As static checking does not need a build of the Sage library, for PRs that do not make any changes to packages, there's nothing to build, and the workflow gives a fast turnaround just after 10 minutes. For applying the CI fixes from blocker tickets, this workflow uses the technique favored in sagemath#36349. The workflow **build.yml** first launches a job: - **test-new:** It builds incrementally (using a tox-generated `Dockerfile` and https://github.com/marketplace/actions/build-and-push- docker-images) and does the quick incremental test. This completes within 10 to 20 minutes when there's no change. After this is completed, more jobs are launched: - **test-mod:** It again builds incrementally and tests a modularized distribution. Later (with more from sagemath#35095), more jobs will be added to this matrix job for other distributions. - **test-long:** It again builds incrementally and runs the long test. The workflows **doc-build.yml** and **doc-build-pdf.yml** again build incrementally and then build the documentation. The diffing code for the HTML documentation now runs in the host, not the container, which simplifies things. (To show that diffing still works, we include a small change to the Sage library.) Splitting the workflow jobs implements @kwankyu's suggestion from: - sagemath#35652 (comment) (Fixes sagemath#35814) The steps "again builds incrementally" actually use the GH Actions cache, https://docs.docker.com/build/ci/github-actions/cache/#cache- backend-api. When nothing is cached and the 3 workflows are launched in parallel, they may each build the same thing. But when there's congestion that leads to the workflows to be run serially, the 2nd and 3rd workflow will be able to use the cache from the 1st workflow. This elasticity may be helpful in reducing congestion. There is a rather small per-project limit of 10 GB for this cache, so we'll have to see how effectively caching works in practice. See https://github.com/sagemath/sage/actions/caches   ### 📝 Checklist     - [x] The title is concise, informative, and self-explanatory. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies  - Depends on sagemath#36938 (merged here) - Depends on sagemath#36951 (merged here) - Depends on sagemath#37351 (merged here) - Depends on sagemath#37750 (merged here)  URL: sagemath#36498 Reported by: Matthias Köppe Reviewer(s): Kwankyu Lee, Matthias Köppe

@kwankyu

…arate jobs for pyright, build, modularized tests, long tests    Running the containers explicitly, instead of using the declarative `container:` feature of GH Actions gives us more control: - we can create more space on the host if necessary; we just scraped by an out of space condition in sagemath#36473 / sagemath#36469 (comment) - we can run some operations outside of the container but in the same job; this will make the separate "Get CI fixes" jobs unnecessary, addressing the cosmetic concerns from sagemath#36338 (comment), sagemath#36349 - it enables caching between the various workflows (as first discussed in sagemath#36446). We split out static type checking with pyright into its separate workflow: - **pyright.yml**: As static checking does not need a build of the Sage library, for PRs that do not make any changes to packages, there's nothing to build, and the workflow gives a fast turnaround just after 10 minutes. For applying the CI fixes from blocker tickets, this workflow uses the technique favored in sagemath#36349. The workflow **build.yml** first launches a job: - **test-new:** It builds incrementally (using a tox-generated `Dockerfile` and https://github.com/marketplace/actions/build-and-push- docker-images) and does the quick incremental test. This completes within 10 to 20 minutes when there's no change. After this is completed, more jobs are launched: - **test-mod:** It again builds incrementally and tests a modularized distribution. Later (with more from sagemath#35095), more jobs will be added to this matrix job for other distributions. - **test-long:** It again builds incrementally and runs the long test. The workflows **doc-build.yml** and **doc-build-pdf.yml** again build incrementally and then build the documentation. The diffing code for the HTML documentation now runs in the host, not the container, which simplifies things. (To show that diffing still works, we include a small change to the Sage library.) Splitting the workflow jobs implements @kwankyu's suggestion from: - sagemath#35652 (comment) (Fixes sagemath#35814) The steps "again builds incrementally" actually use the GH Actions cache, https://docs.docker.com/build/ci/github-actions/cache/#cache- backend-api. When nothing is cached and the 3 workflows are launched in parallel, they may each build the same thing. But when there's congestion that leads to the workflows to be run serially, the 2nd and 3rd workflow will be able to use the cache from the 1st workflow. This elasticity may be helpful in reducing congestion. There is a rather small per-project limit of 10 GB for this cache, so we'll have to see how effectively caching works in practice. See https://github.com/sagemath/sage/actions/caches   ### 📝 Checklist     - [x] The title is concise, informative, and self-explanatory. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies  - Depends on sagemath#36938 (merged here) - Depends on sagemath#36951 (merged here) - Depends on sagemath#37351 (merged here) - Depends on sagemath#37750 (merged here) - Depends on sagemath#37277 (merged here)  URL: sagemath#36498 Reported by: Matthias Köppe Reviewer(s): Kwankyu Lee, Matthias Köppe

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Matthias Koeppe added 4 commits May 25, 2023 19:04

.github/workflows/build.yml: First build really incrementally and tes…

4451886

…t changed files

src/sage/doctest/control.py: Make 'sage -t --new' work in git worktrees

2881586

.github/workflows/build.yml: Run non-incremental tests with --long

43fcf4a

.github/workflows/build.yml: Explicitly run bootstrap before the incr…

f9b4412

…emental build

mkoeppe force-pushed the ci_more_incremental branch from a82f6a1 to f9b4412 Compare May 26, 2023 02:04

.github/workflows/build.yml: Explicitly run bootstrap before the incr…

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…emental build (fixup)

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kwankyu added a commit to kwankyu/sage that referenced this pull request May 28, 2023

Copy of pr sagemath#35652

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Matthias Koeppe added 2 commits June 4, 2023 11:52

Merge remote-tracking branch 'upstream/develop' into ci_more_incremental

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.github/workflows/doc-build.yml: Build incrementally

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.github/workflows/doc-build.yml: Build docs non-incrementally

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