MRG, MAINT: Tweak CIs #7943

larsoner · 2020-06-29T13:59:45Z

Permit operators to start newlines in addition to at the end of lines (we have ~575 of these in master) so that we can transition to or at least allow the "new" (as of 2016) way of writing code, as discussed here
Fix or ignore a few style errors in conf.py
Run make flake on the entire codebase not just select folders
Switch to conda for VTK (Following the installation instructions for macOS yields an error message #7939)
Fix CircleCI failures related to numpydoc seen here

NumpyDoc will still cause a failure, I think it needs to be fixed at the NumpyDoc end...

larsoner · 2020-06-29T16:59:45Z

Fixed VTK9 rendering on macOS by disabling depth peeling and anti-aliasing. The remaining bug on my macOS system is that the widget controls do not work because there is a 2x mismatch between their render position and the click position needed to control them. We'll have to see if this is fixable at the PyVista end, or if this is an underlying VTK bug (my money is on the latter).

hoechenberger · 2020-06-29T18:13:49Z

The remaining bug on my macOS system is that the widget controls do not work because there is a 2x mismatch between their render position and the click position needed to control them. We'll have to see if this is fixable at the PyVista end, or if this is an underlying VTK bug (my money is on the latter).

This suggests that there's something off with the conversion between retina pixels and displayed points

mne/cov.py

agramfort · 2020-06-29T19:37:46Z

mne/fixes.py

+
+
+###############################################################################
+# Work around autosummary making bad :class: links


this sucks. It was working with an older version? if so can we rather pin the version rather than crippling our code?

How does this cripple our code? It just replaces a few docstrings. Subclassing like isinstance(x, dict) are still fine. Overhead should be minimal.

The problem is that numpydoc improved the signature extraction, and we hit a bug now with autosummary trying to add effectively:

:class:`v, remove specified key and return the corresponding value.`

to correspond to the D.pop() -> v, remove specified key and return the corresponding value. docstring.

This seemed like the cleanest solution, but I'm open to other ideas.

agramfort · 2020-06-29T19:48:05Z

it's because numpydoc does not parse docstring of std lib?

…

larsoner · 2020-06-29T20:09:19Z

See above -- I think it's because numpydoc passes the stdlib definition unchanged, then autodoc sees the -> in the docstring and assumes that anything after that is only a :class: (hence an autodoc/autosummary bug)

agramfort · 2020-06-29T20:16:02Z

would it make sense to wait for autodoc/autosummary to fix the bug?

…

larsoner · 2020-06-29T20:53:47Z

Maybe, but in the meantime all CircleCI builds will fail. I guess we could roll back numpydoc in the meantime, but no idea how long the autodoc fix will take.

larsoner · 2020-06-29T20:54:39Z

Personally I don't see why the dict_ class is so bad, it just adds one more entry in the MRO...

agramfort · 2020-06-30T06:44:38Z

ok fair enough let's proceed and see in a few weeks/months if we can undo this after a fix upstream

…

hoechenberger · 2020-06-30T07:01:40Z

I agree with @agramfort that it is kind of ugly, but I think it's okay for now :)

hoechenberger

Switch to conda for VTK (Following the installation instructions for macOS yields an error message #7939)

Wait, you're not doing that, unless my brain isn't functioning right bc I haven't had breakfast yet :) You're still using pip to install vtk, and only dropped the version constraint for macOS. This will not fix #7939.

hoechenberger · 2020-06-30T07:19:48Z

I believe this also begs the question if / whether we should switch to conda-forge packages anyway (instead of using defaults / pkgs/main)

$ conda search vtk |grep pkgs/main
vtk                            8.1.0 py27h04d9db9_201  pkgs/main
vtk                            8.1.0 py27h87a2a2b_201  pkgs/main
vtk                            8.1.0 py35h04d9db9_201  pkgs/main
vtk                            8.1.0 py35h87a2a2b_201  pkgs/main
vtk                            8.1.0 py36h04d9db9_201  pkgs/main
vtk                            8.1.0 py36h87a2a2b_201  pkgs/main
vtk                            8.1.1 py27ha9eb873_204  pkgs/main
vtk                            8.1.1 py27hce9f6a2_204  pkgs/main
vtk                            8.1.1 py36ha9eb873_204  pkgs/main
vtk                            8.1.1 py36hce9f6a2_204  pkgs/main
vtk                            8.2.0 py27h9bafd54_200  pkgs/main
vtk                            8.2.0 py36h9bafd54_200  pkgs/main
vtk                            8.2.0 py37h9bafd54_200  pkgs/main
$

hoechenberger · 2020-06-30T08:17:15Z

@larsoner feel free to revert 237e3e1, just want to see if this works…

GuillaumeFavelier · 2020-06-30T08:50:45Z

@hoechenberger I think it follows the news on pyvista/pyvistaqt#16 (comment) and pyvista/pyvistaqt#15 (comment)

Fetching vtk 9.0.1 on PyPi for every OS could solve the problem.

hoechenberger · 2020-06-30T09:18:10Z

Fetching vtk 9.0.1 on PyPi for every OS could solve the problem.

Ok so we only need to pin VTK to >=9.0.1?

GuillaumeFavelier · 2020-06-30T09:19:41Z

For MacOS at least, yes

This reverts commit 237e3e1.

GuillaumeFavelier · 2020-06-30T10:27:45Z

The failures of the notebook job are note related, see #7944

GuillaumeFavelier · 2020-06-30T12:35:31Z

The Windows 3.7 conda job on Azure complains that pytest is not a command. It's not installed?

'pytest' is not recognized as an internal or external command,
operable program or batch file.

agramfort · 2020-06-30T12:51:53Z

try: python -m pytest see https://docs.pytest.org/en/stable/usage.html

larsoner · 2020-06-30T12:55:52Z

The command failing is often an indicator that the install still failed (but didn't error out for some reason)

GuillaumeFavelier · 2020-06-30T13:02:10Z

I pushed again, it seems there was indeed an error in the installation.

GuillaumeFavelier · 2020-06-30T13:15:26Z

Still not happy:

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "d:\a\1\s\conda\lib\site-packages\conda\exceptions.py", line 1079, in __call__
        return func(*args, **kwargs)
      File "d:\a\1\s\conda\lib\site-packages\conda_env\cli\main.py", line 80, in do_call
        exit_code = getattr(module, func_name)(args, parser)
      File "d:\a\1\s\conda\lib\site-packages\conda_env\cli\main_update.py", line 68, in execute
        directory=os.getcwd())
      File "d:\a\1\s\conda\lib\site-packages\conda_env\specs\__init__.py", line 40, in detect
        if spec.can_handle():
      File "d:\a\1\s\conda\lib\site-packages\conda_env\specs\yaml_file.py", line 18, in can_handle
        self._environment = env.from_file(self.filename)
      File "d:\a\1\s\conda\lib\site-packages\conda_env\env.py", line 151, in from_file
        return from_yaml(yamlstr, filename=filename)
      File "d:\a\1\s\conda\lib\site-packages\conda_env\env.py", line 136, in from_yaml
        data = yaml_load_standard(yamlstr)
      File "d:\a\1\s\conda\lib\site-packages\conda\common\serialize.py", line 76, in yaml_load_standard
        return yaml.load(string, Loader=yaml.Loader, version="1.2")
      File "d:\a\1\s\conda\lib\site-packages\ruamel_yaml\main.py", line 640, in load
        return loader._constructor.get_single_data()  # type: ignore
      File "d:\a\1\s\conda\lib\site-packages\ruamel_yaml\constructor.py", line 102, in get_single_data
        node = self.composer.get_single_node()
      File "d:\a\1\s\conda\lib\site-packages\ruamel_yaml\composer.py", line 75, in get_single_node
        document = self.compose_document()
      File "d:\a\1\s\conda\lib\site-packages\ruamel_yaml\composer.py", line 96, in compose_document
        node = self.compose_node(None, None)
      File "d:\a\1\s\conda\lib\site-packages\ruamel_yaml\composer.py", line 132, in compose_node
        node = self.compose_mapping_node(anchor)
      File "d:\a\1\s\conda\lib\site-packages\ruamel_yaml\composer.py", line 194, in compose_mapping_node
        item_value = self.compose_node(node, item_key)
      File "d:\a\1\s\conda\lib\site-packages\ruamel_yaml\composer.py", line 130, in compose_node
        node = self.compose_sequence_node(anchor)
      File "d:\a\1\s\conda\lib\site-packages\ruamel_yaml\composer.py", line 163, in compose_sequence_node
        node.value.append(self.compose_node(node, index))
      File "d:\a\1\s\conda\lib\site-packages\ruamel_yaml\composer.py", line 132, in compose_node
        node = self.compose_mapping_node(anchor)
      File "d:\a\1\s\conda\lib\site-packages\ruamel_yaml\composer.py", line 194, in compose_mapping_node
        item_value = self.compose_node(node, item_key)
      File "d:\a\1\s\conda\lib\site-packages\ruamel_yaml\composer.py", line 130, in compose_node
        node = self.compose_sequence_node(anchor)
      File "d:\a\1\s\conda\lib\site-packages\ruamel_yaml\composer.py", line 162, in compose_sequence_node
        while not self.parser.check_event(SequenceEndEvent):
      File "d:\a\1\s\conda\lib\site-packages\ruamel_yaml\parser.py", line 144, in check_event
        self.current_event = self.state()
      File "d:\a\1\s\conda\lib\site-packages\ruamel_yaml\parser.py", line 519, in parse_indentless_sequence_entry
        token.move_comment(self.scanner.peek_token())
      File "d:\a\1\s\conda\lib\site-packages\ruamel_yaml\scanner.py", line 173, in peek_token
        self.fetch_more_tokens()
      File "d:\a\1\s\conda\lib\site-packages\ruamel_yaml\scanner.py", line 310, in fetch_more_tokens
        % utf8(ch), self.reader.get_mark())
    ruamel_yaml.scanner.ScannerError: while scanning for the next token
    found character '\t' that cannot start any token
      in "<unicode string>", line 35, column 44:
         ... 0.1; platform_system == "Darwin"		
                                             ^ (line: 35)

There is a tab in the file XD

environment.yml

agramfort · 2020-06-30T14:57:54Z

how do we proceed? we have 2 PRs that are red but collectively could be green?

GuillaumeFavelier · 2020-06-30T15:02:34Z

I branched out in #7944. If it makes things easier, I can integrate it in here?

agramfort · 2020-06-30T15:13:12Z

ok for me

…

agramfort · 2020-06-30T19:59:53Z

thx a lot @larsoner and @GuillaumeFavelier !

* upstream/master: (30 commits) MRG: Add remove_labels to _Brain (mne-tools#7964) Add get_picked_points (mne-tools#7963) ENH: Add OpenGL info to mne sys_info (mne-tools#7976) [MRG] Fix reject_tmin and reject_tmax for reject_by_annotation in mne.Epochs (mne-tools#7967) mrg: Add scalar mult and div operators for AverageTFR (mne-tools#7957) MRG, MAINT: Cleaner workaround for Sphinx linking issue (mne-tools#7970) MRG, ENH: Speed up epochs.copy (mne-tools#7968) MRG, BUG: Allow ref mags to have a comp grade (mne-tools#7965) do not forget to pass adjacency (mne-tools#7961) [MRG] fix Issue with stc.project after restricting to a label (mne-tools#7950) Only process nirx event file if present (mne-tools#7951) MRG+1: BUG: info['bads'] order shouldn't matter in write_evokeds() (mne-tools#7954) Fix some small glitches introduced via mne-tools#7845 (mne-tools#7952) Add time player (mne-tools#7940) MAINT: Clean up VTK9 offset array [circle front] (mne-tools#7953) MAINT: Skip a few more on macOS (mne-tools#7948) fix links [skip travis] (mne-tools#7949) MRG, MAINT: Tweak CIs (mne-tools#7943) MRG, BUG: Fix vector scaling (mne-tools#7934) MRG, VIZ, BUG: handle CSD channel type when topo plotting (mne-tools#7935) ...

larsoner added 3 commits June 29, 2020 09:59

MAINT: Tweak CIs [skip travis]

8f56362

FIX: Docstrings [circle front]

af50a1f

FIX: Fix for darwin [circle front]

9dde104

FIX: check [circle front]

9c1a515

larsoner changed the title ~~WIP, MAINT: Tweak CIs~~ MRG, MAINT: Tweak CIs Jun 29, 2020

hoechenberger reviewed Jun 29, 2020

View reviewed changes

mne/cov.py Outdated Show resolved Hide resolved

FIX: Cruft [circle front]

cf400a0

hoechenberger approved these changes Jun 29, 2020

View reviewed changes

agramfort reviewed Jun 29, 2020

View reviewed changes

hoechenberger requested changes Jun 30, 2020

View reviewed changes

Install conda packages from conda-forge

237e3e1

hoechenberger added 2 commits June 30, 2020 11:37

Revert "Install conda packages from conda-forge"

ffb1dac

This reverts commit 237e3e1.

Pin VTK to >=9.0.1 in macOS

b3784ac

TST: Try python -m pytest

38f21fd

Try again

80738d2

Remove \t in environment

e6fce9a

larsoner commented Jun 30, 2020

View reviewed changes

environment.yml Outdated Show resolved Hide resolved

Bump minimum requirement for vtk to 9.0.1

1f329c1

hoechenberger approved these changes Jun 30, 2020

View reviewed changes

hoechenberger mentioned this pull request Jun 30, 2020

[WIP] Use conda-forge packages when creating environment #7946

Closed

GuillaumeFavelier approved these changes Jun 30, 2020

View reviewed changes

Use nbclient for notebook testing

c23fd0c

larsoner mentioned this pull request Jun 30, 2020

MRG, MNT: Migrate to nbclient for notebook testing #7944

Closed

agramfort merged commit b04ff04 into mne-tools:master Jun 30, 2020

larsoner deleted the cis branch June 30, 2020 20:04



		###############################################################################
		# Work around autosummary making bad :class: links

MRG, MAINT: Tweak CIs #7943

MRG, MAINT: Tweak CIs #7943

Uh oh!

Conversation

larsoner commented Jun 29, 2020

Uh oh!

larsoner commented Jun 29, 2020

Uh oh!

hoechenberger commented Jun 29, 2020

Uh oh!

Uh oh!

agramfort Jun 29, 2020

Choose a reason for hiding this comment

Uh oh!

larsoner Jun 29, 2020

Choose a reason for hiding this comment

Uh oh!

agramfort commented Jun 29, 2020 via email

Uh oh!

larsoner commented Jun 29, 2020

Uh oh!

agramfort commented Jun 29, 2020 via email

Uh oh!

larsoner commented Jun 29, 2020

Uh oh!

larsoner commented Jun 29, 2020

Uh oh!

agramfort commented Jun 30, 2020 via email

Uh oh!

hoechenberger commented Jun 30, 2020

Uh oh!

hoechenberger left a comment

Choose a reason for hiding this comment

Uh oh!

hoechenberger commented Jun 30, 2020 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

hoechenberger commented Jun 30, 2020

Uh oh!

GuillaumeFavelier commented Jun 30, 2020

Uh oh!

hoechenberger commented Jun 30, 2020

Uh oh!

GuillaumeFavelier commented Jun 30, 2020

Uh oh!

GuillaumeFavelier commented Jun 30, 2020

Uh oh!

GuillaumeFavelier commented Jun 30, 2020 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

agramfort commented Jun 30, 2020 via email

Uh oh!

larsoner commented Jun 30, 2020

Uh oh!

GuillaumeFavelier commented Jun 30, 2020

Uh oh!

GuillaumeFavelier commented Jun 30, 2020 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

Uh oh!

agramfort commented Jun 30, 2020

Uh oh!

GuillaumeFavelier commented Jun 30, 2020

Uh oh!

agramfort commented Jun 30, 2020 via email

Uh oh!

agramfort commented Jun 30, 2020

Uh oh!

Uh oh!

hoechenberger commented Jun 30, 2020 •

edited

Loading

GuillaumeFavelier commented Jun 30, 2020 •

edited

Loading

GuillaumeFavelier commented Jun 30, 2020 •

edited

Loading