[WIP]cran support #423

marcelotrevisani · 2023-01-17T10:01:38Z

Initial CRAN support based on @ForgottenProgramme PR (#349)

Co-authored-by: Marcelo Duarte Trevisani <marcelotrevisani@users.noreply.github.com>

…crapping functions

marcelotrevisani · 2023-01-17T10:11:10Z

simple example for future 1.26.1

{% set name = "future" %}
{% set version = "1.26.1" %}

package:
  name: r-{{ name }}
  version: '{{ version }}'

source:
  url: https://cran.r-project.org/src/contrib/Archive/future/future_{{ version }}.tar.gz
  sha256: a35c0bdae86265ebe86119231802b6fbf7b1d533b57cb423d8483fbe779390d5

build:
  number: 0
  script: R CMD INSTALL --build .
  rpaths:
    - lib/R/lib/
    - lib/

requirements:
  host:
    - r-base
    - r-digest
    - r-globals >=0.15.0
    - r-listenv >=0.8.0
    - r-parallel
    - r-parallelly >=1.30.0
    - r-tools
    - r-utils
  run:
    - r-base
    - r-digest
    - r-globals >=0.15.0
    - r-listenv >=0.8.0
    - r-parallel
    - r-parallelly >=1.30.0
    - r-tools
    - r-utils

test:
  commands:
    - $R -e "library('future')"  # [not win]
    - "\"%R%\" -e \"library('future')\""  # [win]

about:
  home: https://future.futureverse.org, https://github.com/HenrikBengtsson/future
  summary: The purpose of this package is to provide a lightweight and unified Future API for sequential and parallel processing of R expression via futures.  The simplest way to evaluate an expression in parallel is to use `x %<-% { expression }` with `plan(multisession)`. This package implements sequential, multicore, multisession, and cluster futures.  With these, R expressions can be evaluated on the local machine, in parallel a set of local machines, or distributed on a mix of local and remote machines. Extensions to this package implement additional backends for processing futures via compute
    cluster schedulers, etc. Because of its unified API, there is no need to modify any code in order switch from sequential on the local machine to, say, distributed processing on a remote compute cluster. Another strength of this package is that global variables and functions are automatically identified and exported as needed, making it straightforward to tweak existing code to make use of futures.
  license: LGPL-2.1-or-later

ocefpaf · 2023-01-17T10:29:14Z

@mbargull, and anyone from the bioconda team, we would your input here.

codecov-commenter · 2023-01-17T12:10:45Z

Codecov Report

Merging #423 (eaea455) into main (9c3242e) will increase coverage by 0.38%.
The diff coverage is 92.35%.

@@            Coverage Diff             @@
##             main     #423      +/-   ##
==========================================
+ Coverage   91.30%   91.68%   +0.38%     
==========================================
  Files          17       17              
  Lines        1576     1925     +349     
==========================================
+ Hits         1439     1765     +326     
- Misses        137      160      +23

Flag	Coverage Δ
unittests	`91.68% <92.35%> (+0.38%)`	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
setup.py	`0.00% <0.00%> (ø)`
grayskull/base/github.py	`72.83% <72.83%> (ø)`
grayskull/license/discovery.py	`93.81% <72.97%> (-3.33%)`	⬇️
grayskull/strategy/abstract_strategy.py	`83.33% <83.33%> (ø)`
grayskull/strategy/cran.py	`90.05% <90.05%> (ø)`
grayskull/__main__.py	`92.68% <91.76%> (-5.47%)`	⬇️
grayskull/base/factory.py	`90.69% <92.30%> (+0.69%)`	⬆️
grayskull/strategy/py_base.py	`95.43% <95.43%> (ø)`
grayskull/strategy/pypi.py	`97.39% <97.39%> (ø)`
grayskull/utils.py	`98.12% <97.58%> (-1.88%)`	⬇️
... and 9 more

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isuruf · 2023-01-25T15:28:32Z

Why use a less featureful version of conda skeleton cran here? This has multiple issues

No license_file entry
R_ARGS variable is not used
cross-r-base is not added for non compiler recipes
noarch: generic is not used
DISABLE_AUTOBREW is not added

isuruf · 2023-01-25T15:31:57Z

Also, this PR vendors conda-build code and fails to distribute the license

marcelotrevisani · 2023-01-25T16:09:43Z

Why use a less featureful version of conda skeleton cran here? This has multiple issues

No license_file entry

R_ARGS variable is not used

cross-r-base is not added for non compiler recipes

noarch: generic is not used

DISABLE_AUTOBREW is not added

That is just initial support for R, and things can be improved later on. Everything needs a start :)
Part of this work was not done by me, I am happy to add the licence or strip the code off if you point me out which part is a copy from conda-build.
Grayskull in the first versions didn't have all the features for python recipes as well, but it was improved over time.
Your points of missing a few bits are understandable and can be addressed later.

ocefpaf · 2023-01-25T16:13:19Z

Why use a less featureful version of conda skeleton cran here? This has multiple issues

Just to be clear. Every Software starts with less features and increase in complexity with time. The question here is why grayskull instead of conda-build. I guess that b/c the main reason is why we did this for Python recipes. The slow pace of conda-build development and the difficulty to get PRs accepted drove us to create a new recipe generator.

marcelotrevisani · 2023-01-25T16:13:29Z

if you are keen to help to improve that part related to R, we are more than welcome to accept contributions or to open separated issues for it. Thanks!

isuruf · 2023-01-25T16:33:18Z

Every Software starts with less features and increase in complexity with time.

Not all of the features I mentioned are necessary, but generating recipes that have incomplete licensing information is asking for trouble.

The question here is why grayskull instead of conda-build. I guess that b/c the main reason is why we did this for Python recipes. The slow pace of conda-build development and the difficulty to get PRs accepted drove us to create a new recipe generator.

I don't question that. Moving skeletons out of conda-build is good.

From a look at the code here most of the code here is an almost identical copy of the conda-build code. https://github.com/conda-incubator/grayskull/blob/d17444d66ebf50fdb5d97948c7ecfc654b0f68fa/grayskull/strategy/cran.py#L61-L252
And then https://github.com/conda-incubator/grayskull/blob/d17444d66ebf50fdb5d97948c7ecfc654b0f68fa/grayskull/strategy/cran.py#L255-L346 seems like a stripped down version of the conda-build code.

I'm just curious why this is a stripped down version and not all features were not copied.

ForgottenProgramme and others added 27 commits December 24, 2022 05:04

take bits from conda-skeleton code and add cran subparser

0e34c4e

get index

008675d

add cranstrategy abstract class

9b4eb39

add create_r_recipe_from_list method

e938e69

add conditions in parser

8be936f

Fix fetch_data interface

4567d72

remove pip

f333a5b

populate get_cran_metadata func

75dfc80

download tarball

92fabcd

Write downloaded tarball to disk.

f4b68ef

return recipe

2a5d627

format requirements list

d51358c

add comment

4f0888d

Recipe adjustments for constrains in run requirements

0e35e12

add 'r-base' to host and run req everytime

24c760f

sort the package list

62bfaa6

commit errorneous code with comment

3954133

add cran metadata as comment at the top of the recipe

15f166c

add posix and native at the top of the recipe

58d3340

add cli test for cran

c0bd076

Update grayskull/__main__.py

970e5b3

Co-authored-by: Marcelo Duarte Trevisani <marcelotrevisani@users.noreply.github.com>

Update grayskull/strategy/cran.py

efe21ab

Co-authored-by: Marcelo Duarte Trevisani <marcelotrevisani@users.noreply.github.com>

Refactoring structure

f8d4d27

Return with config.yaml

2b2b75c

Improvements related to the scrapping of cran webpage. Add tests to s…

e0b9624

…crapping functions

Improvements in recipe format

7733647

Improvements in recipe order

7b943cd

marcelotrevisani added 2 commits January 17, 2023 10:12

Add script instructions to R recipes

6afdeac

Strip mamba version from workflow

f67eacc

marcelotrevisani added 2 commits January 17, 2023 10:38

Remove typehint for now

52f5341

Mark gh test as xfail

eaea455

marcelotrevisani merged commit 79a7443 into main Jan 21, 2023

marcelotrevisani deleted the fb-cran branch January 21, 2023 22:11

marcelotrevisani mentioned this pull request Jan 21, 2023

R Support [WIP] #349

Closed

13 tasks

ForgottenProgramme mentioned this pull request Jan 23, 2023

Initial R Support in Grayskull #306

Closed

This was referenced Jan 31, 2023

[BUG] Inconsistent name and output directory for R package recipes #437

Closed

Monitoring grayskull support for R package recipes bgruening/conda_r_skeleton_helper#58

Open

dbast mentioned this pull request Jun 6, 2023

Mark skeleton for deprecation. conda/conda-build#4886

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[WIP]cran support #423

[WIP]cran support #423

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[WIP]cran support #423

[WIP]cran support #423

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