skeleton issueshttps://gitlab.kwant-project.org/qt/skeleton/-/issues2024-02-22T10:47:36Zhttps://gitlab.kwant-project.org/qt/skeleton/-/issues/15CI: enable pages out of the box2024-02-22T10:47:36ZAnton AkhmerovCI: enable pages out of the boxhttps://gitlab.kwant-project.org/qt/skeleton/-/issues/14Skeleton structure is outdated2024-01-05T03:30:32ZJuan TorresSkeleton structure is outdatedThe skeleton structure is often disregarded because its purpose is not clear and because many features are outdated.
Some possible changes to make it more useful include:
- new file structure that changes `analysis` into automatic notes...The skeleton structure is often disregarded because its purpose is not clear and because many features are outdated.
Some possible changes to make it more useful include:
- new file structure that changes `analysis` into automatic notes generation
- new gitlab-CI configuration that includes zip generation, tags, latexdiff, website generationhttps://gitlab.kwant-project.org/qt/skeleton/-/issues/13Skeleton setup does not finish2023-10-02T13:26:09ZIsidora ArayaSkeleton setup does not finishI created a repo using the skeleton and ran setup, but it failed. As a result the repo had the README of the skeleton, and I had to change the config file to push into the right repository. Here is the traceback error:
```
(base) tinker...I created a repo using the skeleton and ran setup, but it failed. As a result the repo had the README of the skeleton, and I had to change the config file to push into the right repository. Here is the traceback error:
```
(base) tinkerer@io:~/oal$ ./setup
/home/tinkerer/oal/./setup:31: DeprecationWarning:
Direct access to constants as 'gitlab.DEVELOPER_ACCESS' is deprecated and will be removed in a future major python-gitlab release. Please see the usage of constants in the 'gitlab.const' module instead. (python-gitlab: /opt/conda/lib/python3.10/site-packages/gitlab/__init__.py:44)
BRANCH_PROTECTION_LEVEL = gitlab.DEVELOPER_ACCESS
configuring new project oal
enter a Gitlab personal access token (generate here https://gitlab.kwant-project.org/profile/personal_access_tokens):
logging in to https://gitlab.kwant-project.org...done
creating project qt/oal on https://gitlab.kwant-project.org...done
creating project qt/oal-data on https://gitlab.kwant-project.org...done
setting API access token for CI.../home/tinkerer/oal/./setup:93: DeprecationWarning: `as_list=False` is deprecated and will be removed in a future version. Use `iterator=True` instead. (python-gitlab: /opt/conda/lib/python3.10/site-packages/gitlab/client.py:870)
snippets = project.snippets.list(as_list=False)
failed
CI jobs will not be able to access the Gitlab API
initializing data repository...done
syncing data repository...failed
Traceback (most recent call last):
File "/home/tinkerer/oal/./setup", line 213, in <module>
main()
File "/home/tinkerer/oal/./setup", line 203, in main
gitlab_repo, gitlab_data_repo = init_project(api_token)
File "/home/tinkerer/oal/./setup", line 131, in init_project
data_repo.remotes.origin.push(refspec='main:main')
File "/opt/conda/lib/python3.10/site-packages/git/remote.py", line 952, in push
return self._get_push_info(proc, progress,
File "/opt/conda/lib/python3.10/site-packages/git/remote.py", line 814, in _get_push_info
proc.wait(stderr=stderr_text)
File "/opt/conda/lib/python3.10/site-packages/git/cmd.py", line 502, in wait
raise GitCommandError(remove_password_if_present(self.args), status, errstr)
git.exc.GitCommandError: Cmd('git') failed due to: exit code(1)
cmdline: git push --porcelain origin main:main
stderr: 'error: src refspec main does not match any
error: failed to push some refs to 'ssh://gitlab.kwant-project.org:443/qt/oal-data.git''
```https://gitlab.kwant-project.org/qt/skeleton/-/issues/12Add maintainer privileges to project creator2020-08-19T09:28:10ZAndré MeloAdd maintainer privileges to project creatorWe can just use [this](https://gitlab.kwant-project.org/computational_physics/mechta/-/blob/master/create_project_workflow.py#L120-127) snippet from `mechta`.We can just use [this](https://gitlab.kwant-project.org/computational_physics/mechta/-/blob/master/create_project_workflow.py#L120-127) snippet from `mechta`.https://gitlab.kwant-project.org/qt/skeleton/-/issues/11Add jupytext as a pre-commit hook?2019-07-21T10:27:24ZAndré MeloAdd jupytext as a pre-commit hook?cc @anton-akhmerov
[Here's an example.](https://jupytext.readthedocs.io/en/latest/using-cli.html#jupytext-as-a-git-pre-commit-hook)
Just a thought, it might get a bit confusing for users.cc @anton-akhmerov
[Here's an example.](https://jupytext.readthedocs.io/en/latest/using-cli.html#jupytext-as-a-git-pre-commit-hook)
Just a thought, it might get a bit confusing for users.https://gitlab.kwant-project.org/qt/skeleton/-/issues/10Access token information is outdated2022-08-06T20:32:32ZAndré MeloAccess token information is outdatedTo get an access token it is now necessary to go to the [Personal access tokens](https://gitlab.kwant-project.org/profile/personal_access_tokens) tab under User settings and then generate a temporary token.To get an access token it is now necessary to go to the [Personal access tokens](https://gitlab.kwant-project.org/profile/personal_access_tokens) tab under User settings and then generate a temporary token.https://gitlab.kwant-project.org/qt/skeleton/-/issues/9building notes fails on producing diff pdf2018-11-12T12:51:11ZRafal Skolasinskibuilding notes fails on producing diff pdfIt happened for [this](https://gitlab.kwant-project.org/qt/r-j-skolasinski/lowdin/-/jobs/31152) job in Lowdin project:
```bash
fatal: Path 'notes/notes.tex' exists on disk, but not in 'f0dbad2df9cec3895860bf91ca9c43de39d262e3'.
```
It i...It happened for [this](https://gitlab.kwant-project.org/qt/r-j-skolasinski/lowdin/-/jobs/31152) job in Lowdin project:
```bash
fatal: Path 'notes/notes.tex' exists on disk, but not in 'f0dbad2df9cec3895860bf91ca9c43de39d262e3'.
```
It is surprising for me why as this file shouldn't be present in last good build and therefore conditional block
```yml
- if [ "$LAST_GOOD_SHA" ] && [ "$DIFF" ]; then
- git show $LAST_GOOD_SHA:$CWD/$tex > old_$tex
- latexdiff old_$tex $tex > diff_$tex
- rm old_$tex
- latexmk -pdf diff_$tex
- fi
```
should not be executed.
It's the first time I saw something like this so maybe just something weird happened in this project. I will report here if I see the issue again.https://gitlab.kwant-project.org/qt/skeleton/-/issues/8CI tweaks2024-01-03T12:56:57ZAnton AkhmerovCI tweaksObserving how skeleton is used within the group, I suggest to:
* throw in a conditional `conda install environment.yml` and `pip install requirements.txt` if a project needs additional packages
* mark all the tasks as "may fail": while c...Observing how skeleton is used within the group, I suggest to:
* throw in a conditional `conda install environment.yml` and `pip install requirements.txt` if a project needs additional packages
* mark all the tasks as "may fail": while compiling the notes makes sense after the analysis step, we don't want it to be not executed when it could as well not use any of the previous results.https://gitlab.kwant-project.org/qt/skeleton/-/issues/7run analysis script fails2018-06-24T13:18:46ZAnton Akhmerovrun analysis script failsI believe this is because different lines in gitlab CI are executed separately, and not as a single script (therefore a bash loop becomes broken).I believe this is because different lines in gitlab CI are executed separately, and not as a single script (therefore a bash loop becomes broken).https://gitlab.kwant-project.org/qt/skeleton/-/issues/6run notebook filters only for diff or add2018-07-13T08:46:08ZRafal Skolasinskirun notebook filters only for diff or addRight now notebook filters run also when ``git status`` command is issued.
For many modified notebooks this add significant lag that affect the workflow.Right now notebook filters run also when ``git status`` command is issued.
For many modified notebooks this add significant lag that affect the workflow.https://gitlab.kwant-project.org/qt/skeleton/-/issues/5generalise setup to work with list of submodules2018-04-03T14:41:44ZRafal Skolasinskigeneralise setup to work with list of submodulesIt would be nice if ``setup`` could be able to properly pull and configure other submodules than ``data``.It would be nice if ``setup`` could be able to properly pull and configure other submodules than ``data``.https://gitlab.kwant-project.org/qt/skeleton/-/issues/4namespace update2022-08-06T20:32:32ZAnton Akhmerovnamespace updateFrom now on, every group user will get their own subgroup within qt (see https://gitlab.kwant-project.org/qt/qt-org). The new projects should then be created inside that namespace, and no sharing is needed anymore.From now on, every group user will get their own subgroup within qt (see https://gitlab.kwant-project.org/qt/qt-org). The new projects should then be created inside that namespace, and no sharing is needed anymore.https://gitlab.kwant-project.org/qt/skeleton/-/issues/3setup should refuse to run if readme is unmodified2017-10-26T09:54:54ZAnton Akhmerovsetup should refuse to run if readme is unmodifiedOr at least we should query if the user really wants a blank readme.Or at least we should query if the user really wants a blank readme.https://gitlab.kwant-project.org/qt/skeleton/-/issues/2Clean notebooks feature of new project skeleton2022-08-06T20:32:32ZPablo PiskunowClean notebooks feature of new project skeletonI see the following error when adding a notebook to a git repository built with the skeleton from the Wiki (https://gitlab.kwant-project.org/qt/admin-notes/wikis/new_project).
```
Traceback (most recent call last):
File "/home/pablo/...I see the following error when adding a notebook to a git repository built with the skeleton from the Wiki (https://gitlab.kwant-project.org/qt/admin-notes/wikis/new_project).
```
Traceback (most recent call last):
File "/home/pablo/miniconda3/envs/python3/bin/jupyter-nbconvert", line 6, in <module>
sys.exit(nbconvert.nbconvertapp.main())
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/jupyter_core/application.py", line 267, in launch_instance
return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/nbconvert/nbconvertapp.py", line 313, in start
self.convert_notebooks()
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/nbconvert/nbconvertapp.py", line 471, in convert_notebooks
self.exporter = cls(config=self.config)
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/nbconvert/exporters/exporter.py", line 103, in __init__
self._init_preprocessors()
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/nbconvert/exporters/exporter.py", line 253, in _init_preprocessors
self.register_preprocessor(preprocessor)
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/nbconvert/exporters/exporter.py", line 219, in register_preprocessor
return self.register_preprocessor(preprocessor_cls, enabled)
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/nbconvert/exporters/exporter.py", line 232, in register_preprocessor
self.register_preprocessor(preprocessor(parent=self), enabled)
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/nbconvert/preprocessors/base.py", line 41, in __init__
super(Preprocessor, self).__init__(**kw)
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/nbconvert/utils/base.py", line 29, in __init__
super(NbConvertBase, self).__init__(**kw)
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/traitlets/config/configurable.py", line 84, in __init__
self.config = config
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/traitlets/traitlets.py", line 585, in __set__
self.set(obj, value)
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/traitlets/traitlets.py", line 574, in set
obj._notify_trait(self.name, old_value, new_value)
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/traitlets/traitlets.py", line 1139, in _notify_trait
type='change',
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/traitlets/traitlets.py", line 1176, in notify_change
c(change)
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/traitlets/traitlets.py", line 819, in compatible_observer
return func(self, change)
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/traitlets/config/configurable.py", line 186, in _config_changed
self._load_config(change.new, traits=traits, section_names=section_names)
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/traitlets/config/configurable.py", line 153, in _load_config
setattr(self, name, deepcopy(config_value))
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/traitlets/traitlets.py", line 585, in __set__
self.set(obj, value)
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/traitlets/traitlets.py", line 559, in set
new_value = self._validate(obj, value)
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/traitlets/traitlets.py", line 591, in _validate
value = self.validate(obj, value)
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/traitlets/traitlets.py", line 2324, in validate
value = super(List, self).validate(obj, value)
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/traitlets/traitlets.py", line 2238, in validate
value = super(Container, self).validate(obj, value)
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/traitlets/traitlets.py", line 1677, in validate
self.error(obj, value)
File "/home/pablo/miniconda3/envs/python3/lib/python3.5/site-packages/traitlets/traitlets.py", line 1524, in error
raise TraitError(e)
traitlets.traitlets.TraitError: The 'remove_metadata_fields' trait of a ClearOutputPreprocessor instance must be a set, but a value of class 'str' (i.e. '[deletable, editable, collapsed, scrolled]') was specified.
error: external filter jupyter nbconvert --to notebook --ClearOutputPreprocessor.enabled=True --ClearOutputPreprocessor.remove_metadata_fields='[deletable, editable, collapsed, scrolled]' --stdin --stdout failed 1
error: external filter jupyter nbconvert --to notebook --ClearOutputPreprocessor.enabled=True --ClearOutputPreprocessor.remove_metadata_fields='[deletable, editable, collapsed, scrolled]' --stdin --stdout failed
```https://gitlab.kwant-project.org/qt/skeleton/-/issues/1Set master branch so that `developer`s can push2022-08-06T20:32:32ZJoseph WestonSet master branch so that `developer`s can push