Consolidate requirements and repository configuration #789

rocco8773 · 2020-04-22T01:13:53Z

The primary goal here is to consolidate how we define package requirements (build, install, tests, docs, etc.). Right now package requirements/dependencies are declared manually in many of the repository configuration files. After the refactor, dependencies should only be defined in the requirements/*.txt files and the setup.cfg file, with appropriate comments to direct developers. Any configuration file that needs dependencies should refer to the locations just mentioned.

This will most likely include housekeeping of the repository configuration files.

…options.extras_require in setup.cfg

…r options

…der options

…irements directory, which mimics the the dependencies under the "developer" options.extras_require

codecov · 2020-04-22T01:39:43Z

Codecov Report

Merging #789 (d2465d8) into master (4a71ade) will decrease coverage by 0.00%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master     #789      +/-   ##
==========================================
- Coverage   96.91%   96.91%   -0.01%     
==========================================
  Files          70       70              
  Lines        6931     6930       -1     
==========================================
- Hits         6717     6716       -1     
  Misses        214      214

Impacted Files	Coverage Δ
plasmapy/diagnostics/langmuir.py	`93.75% <ø> (ø)`
plasmapy/optional_deps.py	`100.00% <ø> (ø)`

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…ture

namurphy

Looking good so far!

requirements/docs.txt

setup.cfg

requirements/install.txt

… here]

…ment for plasmapy

.readthedocs.yml

plasmapy/diagnostics/langmuir.py

StanczakDominik · 2020-04-22T04:23:48Z

setup.cfg

+developer =
+  # install everything for developers
+  %(docs)s
+  %(extras)s
+  %(tests)s


wow, does that actually work? Sick! I guess the good folks over at sunpy (e.g. Stuart) didn't know about it, see:

PlasmaPy/setup.py

Lines 12 to 13 in 91db401

# Dev is everything

extras["dev"] = list(chain(*extras.values()))

we'll have to dump that, probably, and update the docs th

darn touchpad, that dev is now developer.

Yeah, I noticed this too and had no idea we could do this. I like it!

StanczakDominik · 2020-04-22T07:05:57Z

requirements.txt

@@ -0,0 +1,8 @@
+# all dependencies required to build, run, test, and doucment plasmapy


Suggested change

# all dependencies required to build, run, test, and doucment plasmapy

# all dependencies required to build, run, test, and document PlasmaPy

requirements/install.txt

StanczakDominik · 2020-04-22T07:08:50Z

setup.cfg

-tests =
-  pytest >= 5.1
-theory =
+  # for plasmapy.theory


Suggested change

# for plasmapy.theory

# for plasmapy.formulary

setup.cfg

namurphy · 2020-04-23T18:45:49Z

Astropy now requires Numpy version >= 1.16.0, so we probably ought to update that requirement in this PR to be consistent with them.

namurphy · 2020-04-23T18:47:10Z

requirements/install.txt

+astropy >= 3.1
+colorama >= 0.3
+matplotlib >= 3.2
+numpy >= 1.14


Suggested change

numpy >= 1.14

numpy >= 1.16

Does it, now? That's likely a sign of units issues going away!

namurphy · 2020-04-26T21:44:23Z

I just realized that requirements information will be needed for the CodeMeta file, so it's likely there will be one more place that will need to be updated... This could be done just prior to every release, though.

StanczakDominik · 2021-01-29T08:20:31Z

I've been thinking that this would be worthwhile to prioritise. Would you mind if I picked this up from here?

StanczakDominik · 2021-03-30T10:08:07Z

@namurphy @rocco8773 a question. f150758 claims that the .zenodo.json file is outdated and removes it. Can I ask for some context on that?

I would gladly remove it from the release guidelines 😜

StanczakDominik · 2021-03-30T11:34:35Z

One funny thing I realized with with the %(extras)s aprroach to extras in setup.cfg: it concatenates the requirements. So we get h5py a bunch of times. But then pip turns them into a set along the way, I think, so it should be fine.

StanczakDominik · 2021-03-30T11:38:07Z

@rocco8773 I'm not quite sure what you were referring to with the BaPSFlib setup. I cleaned it up as much as I could for now, though.

StanczakDominik · 2021-03-30T11:53:00Z

Two issues that I'd rather leave for the next PR to touch these:

https://github.com/rocco8773/PlasmaPy/blob/7769ee263e7c70353fac9fa3496b1ff2befba90f/setup.cfg#L32-L34

This would probably simplify our conda packaging process a little.

https://github.com/rocco8773/PlasmaPy/blob/7769ee263e7c70353fac9fa3496b1ff2befba90f/tox.ini#L53-L90

I have not yet been able to simplify these, and would definitely like to. I suspect that there might be some way to specify "take the minimum of the range for these extras", maybe a pip install flag... but I don't know yet.

I will turn these into issues once this gets merged.

rocco8773 · 2021-03-30T18:01:34Z

@rocco8773 I'm not quite sure what you were referring to with the BaPSFlib setup. I cleaned it up as much as I could for now, though.

Look how I structured and commented the requirements between the ./requirements/ directory, setup.cfg, and pyproject.toml in BaPSF/bapsflib#47. Basically I'm wanted link back comments so if we make a change to setup.cfg we know to also change X, and visa-versa.

StanczakDominik · 2021-04-01T14:43:48Z

Look how I structured and commented the requirements between the ./requirements/ directory, setup.cfg, and pyproject.toml in BaPSF/bapsflib#47. Basically I'm wanted link back comments so if we make a change to setup.cfg we know to also change X, and visa-versa.

The appropriate comments were already there, just with config.cfg rather than setup.cfg! Anyway, looks like that's done.

StanczakDominik

This has stalled out long enough, and doesn't break stuff; in the interest of getting it through before we have to fix more merge conflicts, let's get it in!

suggestions got addressed!

rocco8773 added 9 commits April 21, 2020 17:33

define structure for defining pkg build requirements

1390be5

define structure for defining pkg runtime/install requirements

82a1374

update url to https and classifiers to include python 3.8

f97b6e8

define extras_require for tests, docs, extras, and developer

64f23de

define requirements/docs.txt and sync with the "docs" option under …

819e446

…options.extras_require in setup.cfg

define requirements/tests.txt and sync with the "tests" option unde…

6f40f77

…r options

define requirements/extras.txt and sync with the "extras" option un…

b89e4f7

…der options

define requirements.txt; this will install all files under the requ…

7611a40

…irements directory, which mimics the the dependencies under the "developer" options.extras_require

remove no longer used .gitmodules

1e668d3

rocco8773 added refactoring ♻️ Improving an implementation without adding new functionality optimization Related to optimizing performance, such as with Cython or Numba labels Apr 22, 2020

rocco8773 requested review from namurphy and StanczakDominik April 22, 2020 01:13

rocco8773 self-assigned this Apr 22, 2020

typo

fa3ccab

rocco8773 added 3 commits April 21, 2020 19:02

make doc requirements also depend on extras

1f087b1

update RTD configuration with comments and current requirements struc…

e5d28bb

…ture

add pytest >= 5.1 to "extras" requirements

a2abd3c

namurphy reviewed Apr 22, 2020

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rocco8773 added 3 commits April 21, 2020 19:57

delete outdated .zenodo.json

f150758

make dependency matplotlib >= 3.2 [matplotlib supports py{36, 37, 38}…

18c22e2

… here]

remove warnings for importing matplotlib, matplotlib is now a require…

31c2527

…ment for plasmapy

StanczakDominik requested changes Apr 22, 2020

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namurphy previously requested changes Apr 23, 2020

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namurphy mentioned this pull request May 1, 2020

Release version 0.4.0 #795

Closed

5 tasks

rocco8773 requested a review from StanczakDominik May 19, 2020 18:32

Merge branch 'master' into consolidate-requirements

6d46c66

github-actions bot added the plasmapy.diagnostics Related to the plasmapy.diagnostics subpackage label Mar 30, 2021

StanczakDominik added 3 commits March 30, 2021 12:39

Silence whining end of line fixer

7a7e547

Remove mpl optional error message from all

762f9df

Bring setup files up to date

e043d4d

StanczakDominik requested review from StanczakDominik and removed request for StanczakDominik March 30, 2021 11:05

StanczakDominik added 2 commits March 30, 2021 13:26

Vastly simplify setup.py!

70fc467

A probably too verbose changelog

7769ee2

StanczakDominik marked this pull request as ready for review March 30, 2021 11:40

StanczakDominik requested a review from a team March 30, 2021 11:42

StanczakDominik added 5 commits April 1, 2021 16:38

Move note on all to extras

5a53ab0

Adjust reqs/docs.txt

7154717

adjust reqs/extras.txt

a935c98

install.txt

7e4bde5

tests.txt

3417a46

StanczakDominik added 2 commits April 19, 2021 19:47

Merge branch 'master' into consolidate-requirements

d0349a5

Post-merge fixes

d2465d8

StanczakDominik approved these changes Apr 19, 2021

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StanczakDominik enabled auto-merge (squash) April 19, 2021 18:02

StanczakDominik merged commit ccca766 into PlasmaPy:master Apr 19, 2021

namurphy mentioned this pull request Sep 23, 2021

Consolidate requirements in a single place #1276

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Consolidate requirements and repository configuration #789

Consolidate requirements and repository configuration #789

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	# Dev is everything
	extras["dev"] = list(chain(*extras.values()))

		@@ -0,0 +1,8 @@
		# all dependencies required to build, run, test, and doucment plasmapy

Consolidate requirements and repository configuration #789

Consolidate requirements and repository configuration #789

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