ENH: Warn about versions in sys_info #12146

larsoner · 2023-10-26T15:44:10Z

This is the best formatting I could find:

Add version check right by where the mne version is reported, and
If outdated, add a line at the end gently suggesting to update

With this change I get:

On dev

On my machine I get:

$ mne sys_info
Platform             Linux-6.2.0-35-generic-x86_64-with-glibc2.37
Python               3.11.4 (main, Jun  9 2023, 07:59:55) [GCC 12.3.0]
Executable           /home/larsoner/python/virtualenvs/base/bin/python3
CPU                  x86_64 (8 cores)
Memory               62.7 GB

Core
├☑ mne               1.6.0.dev154+ga320b631a7.d20231024
│                    ✓ Dev version (latest release: 1.5.1)
├☑ numpy             2.0.0.dev0+git20231025.9f6789c (OpenBLAS 0.3.23.dev with 4 threads)
├☑ scipy             1.12.0.dev0+1888.d7f12d3
...
├☑ mne-bids-pipeline 1.4.0
└☐ unavailable       mne-nirs, mne-features, mne-connectivity, mne-icalabel

On stable

Hacking the code to say I'm on stable the above changes to:

├☑ mne               1.5.1
│                    ✓ On the latest release

Outdated

Hacking the code to fake the latest release to be 1.7 we see the two lines change:

$ mne sys_info
Platform             Linux-6.2.0-35-generic-x86_64-with-glibc2.37
Python               3.11.4 (main, Jun  9 2023, 07:59:55) [GCC 12.3.0]
Executable           /home/larsoner/python/virtualenvs/base/bin/python3
CPU                  x86_64 (8 cores)
Memory               62.7 GB

Core
├☑ mne               1.6.0.dev154+ga320b631a7.d20231024
│                    ✗ A newer version 1.7 is available!
├☑ numpy             2.0.0.dev0+git20231025.9f6789c (OpenBLAS 0.3.23.dev with 4 threads)
├☑ scipy             1.12.0.dev0+1888.d7f12d3
...
├☑ mne-bids-pipeline 1.4.0
└☐ unavailable       mne-nirs, mne-features, mne-connectivity, mne-icalabel

To update to the latest supported release version to get bugfixes and improvements, visit https://mne.tools/stable/install/updating.html

Timeout (default 2s)

If I hack the timeout to be tiny enough that it fails for my system, same

├☑ mne               1.6.0.dev154+ga320b631a7.d20231024
│                    Unable to check latest version on GitHub (2.0 sec timeout)

Todo

Just waiting for feedback before finishing:

Tests
Changelog entry

Closes #12132

drammock

thanks for doing this! My (bikeshedding) nitpicks are:

prefer to have the message on the same line as the reported version (similar to how we put BLAS info in parentheses after reporting numpy version)
instead of an extra check/x-mark in the message, I would consider having the main left-margin checkbox be the indicator, like
- ✓ (installed stable or dev)
- x (installed old version)

drammock · 2023-10-26T18:44:18Z

mne/utils/config.py

+from urllib.error import URLError
+from urllib.request import urlopen
+
+from packaging.version import parse


I'm surprised this passed style checks, shouldn't it fail on import sorting grounds?

This makes it a different import block

larsoner · 2023-10-26T18:56:37Z

prefer to have the message on the same line as the reported version (similar to how we put BLAS info in parentheses after reporting numpy version)

Actually this split is intentional. It gives people two chances to see the version mismatch. If you really want them EDIT: in one place, I guess I'd prefer and can live with them both in a separate message at the bottom since it's more visible than when it's up by mne.

drammock · 2023-10-26T19:02:06Z

prefer to have the message on the same line as the reported version (similar to how we put BLAS info in parentheses after reporting numpy version)

Actually this split is intentional. It gives people two chances to see the version mismatch. If you really want them EDIT: in one place, I guess I'd prefer and can live with them both in a separate message at the bottom since it's more visible than when it's up by mne.

I wasn't being clear. I like that you add a warning-like sentence after the whole results table is done. What I meant was that I don't like the entry for MNE spanning two lines.

larsoner · 2023-10-26T19:13:02Z

So something like:

Platform             Linux-6.2.0-35-generic-x86_64-with-glibc2.37
Python               3.11.4 (main, Jun  9 2023, 07:59:55) [GCC 12.3.0]
Executable           /home/larsoner/python/virtualenvs/base/bin/python3
CPU                  x86_64 (8 cores)
Memory               62.7 GB

Core
├☒ mne               1.6.0.dev154+ga320b631a7.d20231024 (outdated, release 1.7.0 is available!)
├☑ numpy             2.0.0.dev0+git20231025.9f6789c (OpenBLAS 0.3.23.dev with 4 threads)
...
├☑ mne-bids          0.14.dev0
├☑ mne-bids-pipeline 1.4.0
└☐ unavailable       mne-nirs, mne-features, mne-connectivity, mne-icalabel

To update to the latest supported release version to get bugfixes and improvements, visit https://mne.tools/stable/install/updating.html

and for the other variants:

├☑ mne               1.6.0.dev154+ga320b631a7.d20231024 (devel, latest release is 1.5.1)

├☑ mne               1.5.1 (latest release)

├☑ mne               1.6.0.dev154+ga320b631a7.d20231024 (unable to check for latest version on GitHub, 2.0 sec timeout)

drammock · 2023-10-26T19:15:43Z

So something like:

yes exactly!

larsoner · 2023-10-26T19:16:49Z

Okay pushed a commit for that. Just need to add a couple tests and changelog!

larsoner · 2023-10-26T20:23:08Z

Okay tests and changelog updated

drammock

LGTM except for one oversight I think, see below

mne/utils/config.py

Co-authored-by: Daniel McCloy <dan@mccloy.info>

hoechenberger · 2023-10-27T08:39:24Z

We could also query PyPI to ensure the package is already pip-installable by the time we display the message:
https://pypi.python.org/pypi/mne/json

hoechenberger · 2023-10-27T08:48:45Z

@larsoner
Something to consider before merging

I'm behind a corporate firewall that injects a self-signed MITM certificate so it can spy on TLS connections

Which can cause troubles connecting to online services unless one explicitly specifies that one trusts this cert

For example, for Python's requests I have to set the REQUESTS_CA_BUNDLE env var or else connections may fail.
(For Node and conda, it's yet another setting. Yeah, real fun, I tell ya…)

I'd like to try out how this branch behaves in different settings (with and without the env var set; connection from the office and remotely through a VPN; on the host machine and inside a Docker Dev Container) before we merge, just to ensure sys_info doesn't suddenly explode or spit out many lines of error messages

But I won't have time to test before next week

Please hold off merging until then if possible

And please do ping me if you don't hear back from me by Wednesday

Thanks

drammock · 2023-10-27T11:10:12Z

I'd like to try out how this branch behaves in different settings (with and without the env var set; connection from the office and remotely through a VPN; on the host machine and inside a Docker Dev Container) before we merge

Good idea, IMO there is no rush on this one

hoechenberger · 2023-10-30T14:39:53Z

Seems to be working for me, however, I basically immediately see this line when running behind our corporate firewall:

├☑ mne               1.6.0.dev167+gda1747f02 (unable to check for latest version on GitHub, 2.0 sec timeout)

Clearly, 2 sec have not passed, I get this output almost instantaneously

So maybe we should just remove the part of the logging message that mentions the timeout?

hoechenberger · 2023-10-30T14:42:29Z

The exception that occurs is:

URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self-signed certificate in certificate chain (_ssl.c:1006)>

hoechenberger · 2023-10-30T14:46:33Z

… and the solution (on the user's end) is to set the SSL_CERT_FILE env var to the path of the self-signed root certificate.

❯ SSL_CERT_FILE=... mne sys_info
...
├☑ mne               1.6.0.dev167+gda1747f02 (devel, latest release is 1.5.1)
...

mne/utils/config.py

larsoner · 2023-10-30T15:10:44Z

So maybe we should just remove the part of the logging message that mentions the timeout?

Now I triage timeouts, SSL errors, and unknown errors. It seemed reasonable to add some explanation to these cases

hoechenberger · 2023-10-30T15:13:15Z

@larsoner Works! :)

* upstream/main: (35 commits) [DOC] Add documentation for setting montage order (mne-tools#12160) Fix inferring fiducials from EEGLAB (mne-tools#12165) Try to fix ICA Report (mne-tools#12167) BUG: Fix bug with Report.add_ica component number (mne-tools#12156) MAINT: Add rstcheck to CIs and pre-commit (mne-tools#12163) DOC: fix sphinx style typos (mne-tools#12161) MAINT: Fix linkcheck (mne-tools#12162) ENH: Add multiple label support to source_band_induced_power, source_induced_power (mne-tools#12026) Allow automated metadata generation to be bounded by "row events" instead of explicit time windows (mne-tools#12118) ENH: Collapse only in doc gen (mne-tools#12145) [pre-commit.ci] pre-commit autoupdate (mne-tools#12155) BUG: Fix bug with interior points not showing (mne-tools#12148) ENH: Warn about versions in sys_info (mne-tools#12146) Fix in conftest.py (mne-tools#12150) ENH: set color for bad channel with spatial_colors=True (mne-tools#12142) DOC: Better documentation of realign_raw (mne-tools#12135) Add mne-icalabel wildcard (mne-tools#12143) Remove LGTM.com configuration file (mne-tools#12139) DOC: Fix typo found by codespell (mne-tools#12140) DOC: Document governance updates (mne-tools#12133) ...

* upstream/main: (26 commits) FIX: Fix bug with coreg scalars (mne-tools#12164) Changed casting rule in np.clip to allow reading of raw GDF files (mne-tools#12168) [DOC] Add documentation for setting montage order (mne-tools#12160) Fix inferring fiducials from EEGLAB (mne-tools#12165) Try to fix ICA Report (mne-tools#12167) BUG: Fix bug with Report.add_ica component number (mne-tools#12156) MAINT: Add rstcheck to CIs and pre-commit (mne-tools#12163) DOC: fix sphinx style typos (mne-tools#12161) MAINT: Fix linkcheck (mne-tools#12162) ENH: Add multiple label support to source_band_induced_power, source_induced_power (mne-tools#12026) Allow automated metadata generation to be bounded by "row events" instead of explicit time windows (mne-tools#12118) ENH: Collapse only in doc gen (mne-tools#12145) [pre-commit.ci] pre-commit autoupdate (mne-tools#12155) BUG: Fix bug with interior points not showing (mne-tools#12148) ENH: Warn about versions in sys_info (mne-tools#12146) Fix in conftest.py (mne-tools#12150) ENH: set color for bad channel with spatial_colors=True (mne-tools#12142) DOC: Better documentation of realign_raw (mne-tools#12135) Add mne-icalabel wildcard (mne-tools#12143) Remove LGTM.com configuration file (mne-tools#12139) ...

Co-authored-by: Daniel McCloy <dan@mccloy.info>

ENH: Warn about versions in sys_info [ci skip]

145139a

larsoner requested a review from drammock as a code owner October 26, 2023 15:44

larsoner added this to the 1.6 milestone Oct 26, 2023

larsoner mentioned this pull request Oct 26, 2023

DOC: Actively suggest updating MNE to a supported version #12132

Closed

drammock approved these changes Oct 26, 2023

View reviewed changes

FIX: Simplify

85f701f

FIX: Tests

74d78d8

larsoner requested review from agramfort and dengemann as code owners October 26, 2023 20:19

Merge branch 'main' into et

7ecdc8e

drammock reviewed Oct 26, 2023

View reviewed changes

mne/utils/config.py Outdated Show resolved Hide resolved

Update mne/utils/config.py

614f519

Co-authored-by: Daniel McCloy <dan@mccloy.info>

larsoner removed request for agramfort and dengemann October 26, 2023 22:54

larsoner added 2 commits October 26, 2023 22:13

FIX: command

1e3c06d

Merge branch 'main' into et

da1747f

larsoner commented Oct 30, 2023

View reviewed changes

mne/utils/config.py Outdated Show resolved Hide resolved

FIX: Better msg

a395857

larsoner added 2 commits October 30, 2023 11:07

FIX: Decorate

a927ef8

FIX: Unify

1a490bf

drammock approved these changes Oct 30, 2023

View reviewed changes

drammock merged commit 72225b5 into mne-tools:main Oct 30, 2023
28 checks passed

drammock deleted the et branch October 30, 2023 17:17

snwnde pushed a commit to snwnde/mne-python that referenced this pull request Mar 20, 2024

ENH: Warn about versions in sys_info (mne-tools#12146)

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Co-authored-by: Daniel McCloy <dan@mccloy.info>

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ENH: Warn about versions in sys_info #12146

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ENH: Warn about versions in sys_info #12146

ENH: Warn about versions in sys_info #12146

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On dev

On stable

Outdated

Timeout (default 2s)

Todo

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