feat: Add API to download likelihood patchset archives #1046

matthewfeickert · 2020-08-22T01:02:24Z

Description

Resolves #1045

$ pyhf contrib download --help
Usage: pyhf contrib download [OPTIONS] [ARCHIVE_URL] [OUTPUT_DIRECTORY]

  Download the patchset archive from the remote URL and extract it in a
  directory at the path given.

  Example:

  .. code-block:: shell

      $ pyhf contrib download --verbose
      https://www.hepdata.net/record/resource/1408476?view=true 1Lbb-
      likelihoods

          1Lbb-likelihoods/patchset.json
          1Lbb-likelihoods/README.md
          1Lbb-likelihoods/BkgOnly.json

  Raises:     :class:`~pyhf.exceptions.InvalidArchiveHost`: if the provided
  archive host name is not known to be valid

Options:
  -v, --verbose   Enables verbose mode
  -f, --force     Force download from non-approved host
  -c, --compress  Keep the archive in a compressed tar.gz form
  -h, --help      Show this message and exit.

CLI API Example:

$ pyhf contrib download https://www.hepdata.net/record/resource/1408476?view=true 1Lbb-likelihoods
$ ls 1Lbb-likelihoods/
BkgOnly.json  patchset.json  README.md
$ rm -rf 1Lbb-likelihoods && pyhf contrib download -v https://www.hepdata.net/record/resource/1408476?view=true 1Lbb-likelihoods
1Lbb-likelihoods/patchset.json
1Lbb-likelihoods/README.md
1Lbb-likelihoods/BkgOnly.json
$ pyhf contrib download --compress https://www.hepdata.net/record/resource/1408476?view=true 1Lbb-likelihoods.tar.gz
$ file 1Lbb-likelihoods.tar.gz 
1Lbb-likelihoods.tar.gz: gzip compressed data, from Unix, original size modulo 2^32 6177792

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For the PR Assignees:

Summarize commit messages into a comprehensive review of the PR

* Add download command to Python contrib API
* Add download command to pyhf CLI API and add contrib group
* Add pyhf custom exception if an untrusted archive host is given
* Add tests of Python and CLI API versions of contrib download
   - Thanks to Anthony Sottile (@asottile) for advice: https://youtu.be/PXu3KCMT3l4
* Add requests as dependency of contrib extra
* Add Python contrib API to docs

codecov · 2020-08-22T01:04:00Z

Codecov Report

Merging #1046 into master will increase coverage by 0.04%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master    #1046      +/-   ##
==========================================
+ Coverage   96.83%   96.87%   +0.04%     
==========================================
  Files          60       62       +2     
  Lines        3507     3556      +49     
  Branches      504      510       +6     
==========================================
+ Hits         3396     3445      +49     
  Misses         68       68              
  Partials       43       43

Flag	Coverage Δ
#unittests	`96.87% <100.00%> (+0.04%)`	⬆️

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Impacted Files	Coverage Δ
src/pyhf/cli/__init__.py	`100.00% <100.00%> (ø)`
src/pyhf/cli/cli.py	`100.00% <100.00%> (ø)`
src/pyhf/cli/contrib.py	`100.00% <100.00%> (ø)`
src/pyhf/contrib/utils.py	`100.00% <100.00%> (ø)`
src/pyhf/exceptions/__init__.py	`100.00% <100.00%> (ø)`

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src/pyhf/cli/patchset.py

matthewfeickert · 2020-08-22T19:42:23Z

@kratsg Given your comment on Issue #1045 RE: implementing Issue #947 what are your thoughts on this PR?

It seems to me that having something like this PRs functionality of downloading a tarball and then extracting it into a directory is still in scope of pyhf utilities, but susyudio is another separate planned library(?) given that your example starts with import susyudio. Is that correct?

src/pyhf/cli/patchset.py

src/pyhf/cli/contrib.py

matthewfeickert · 2020-09-13T08:00:28Z

tests/test_scripts.py

+    # hide
+    CACHE_MODULE, sys.modules[module_name] = sys.modules[module_name], None


I guess the only other thing to think about is if this should be made into a decorator.

kratsg

what if pyhf contrib download was hidden away if it didn't import correctly?

additionally, there should be a non-script/CLI test to check the python API itself.

matthewfeickert · 2020-09-15T05:08:37Z

additionally, there should be a non-script/CLI test to check the python API itself.

Hm. Maybe I misunderstand what you mean, but we don't have a public Python API for this, we only have the CLI API that's exposed.

kratsg · 2020-09-15T10:26:03Z

Hm. Maybe I misunderstand what you mean, but we don't have a public Python API for this, we only have the CLI API that's exposed.

It would generally make sense that we don't provide a CLI for anything that does not have a python API (for consistency) no? Maybe we need the python API first.

matthewfeickert · 2020-09-15T14:11:23Z

It would generally make sense that we don't provide a CLI for anything that does not have a python API (for consistency) no? Maybe we need the python API first.

I think I generally agree with that statement but if you're at the Python API do you really care about extracting files into directories rather than just reading them out from the in memory representation of the tarfile? I guess what you're thinking though is that if you wanted to script the download and unpacking of multiple likelihoods through the Python API you should be able to do that as well (correct?).

kratsg · 2020-09-15T19:04:01Z

I think I generally agree with that statement but if you're at the Python API do you really care about extracting files into directories rather than just reading them out from the in memory representation of the tarfile? I guess what you're thinking though is that if you wanted to script the download and unpacking of multiple likelihoods through the Python API you should be able to do that as well (correct?).

Yes, or likely -- someone will want to parallelize and do a signal grid... But I'm realizing that this doesn't make sense given we only really ever have two files per grid anyway (bkgonly + patchset)...

src/pyhf/cli/contrib.py

The removal seems to not be effective in masking requests

This reverts commit 3af9b19. This is hard to test at the moment as don't have any of these, so hold off

* Remove contrib download defaults for arguments ARCHIVE_URL OUTPUT_DIRECTORY * Amends PR #1046

* Migrate contrib download code from cli module to contrib module - Unify all of the contrib code in a single contrib module for easier factoring out and bookkeeping * Use DOI URL for all contrib download docstring examples * Amends PR #1046

matthewfeickert added feat/enhancement New feature or request CLI Affects the CLI API labels Aug 22, 2020

matthewfeickert self-assigned this Aug 22, 2020

matthewfeickert commented Aug 22, 2020

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matthewfeickert marked this pull request as ready for review August 22, 2020 08:29

matthewfeickert requested review from kratsg and lukasheinrich August 22, 2020 08:29

matthewfeickert force-pushed the feat/add-patchset-download-cli-api branch from cc53772 to 3b8fb74 Compare August 31, 2020 22:43

matthewfeickert commented Sep 2, 2020

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matthewfeickert force-pushed the feat/add-patchset-download-cli-api branch from 3b8fb74 to 8258466 Compare September 2, 2020 22:42

matthewfeickert mentioned this pull request Sep 4, 2020

Add CLI API to download likelihood patchset archives from HEPData #1045

Closed

matthewfeickert force-pushed the feat/add-patchset-download-cli-api branch 2 times, most recently from 32e35be to f6f9ce8 Compare September 11, 2020 14:56

kratsg approved these changes Sep 11, 2020

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matthewfeickert requested a review from kratsg September 12, 2020 07:21

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matthewfeickert force-pushed the feat/add-patchset-download-cli-api branch from 840b567 to 2317bab Compare September 13, 2020 07:42

matthewfeickert commented Sep 13, 2020

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matthewfeickert marked this pull request as draft September 14, 2020 06:09

matthewfeickert commented Sep 17, 2020

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matthewfeickert force-pushed the feat/add-patchset-download-cli-api branch from afc202c to 90f9e80 Compare September 17, 2020 05:50

matthewfeickert added the API Changes the public API label Sep 17, 2020

matthewfeickert added 21 commits October 9, 2020 16:52

Add test for missing requests module

75e1889

Guard contrib functions beyond cli in try except

6e8ccd7

Update tests for guarded pyhf contrib download

3797d44

Add Contrib to Python API docs

7e23fa9

Correct mislabeling of analysis

8bddb71

Add Python API to contrib download

3fcbcba

Wrap Python API in CLI API

3717003

Allow for POSIX tar archives that are not gzip

83bd2ef

Sort to avoid doctest error

d04564c

Fixup of test_scripts

ef71fca

The removal seems to not be effective in masking requests

Use del of modules to force state

506e59e

Fix typo

0ca56bc

Use mock after watching Anthony Sottile's video

39b8feb

Revert "Allow for POSIX tar archives that are not gzip"

8fc005a

This reverts commit 3af9b19. This is hard to test at the moment as don't have any of these, so hold off

Add TOOD for removal of Python 3.6

0af5ba4

Add note

560fe64

Use log.error instead of print

2afb313

Make pyflakes happy

0e05559

ERROR not INFO

8178fa3

Remove unneeded variable

d8e2761

Don't rely on newlines being in output given systems

b72e399

matthewfeickert force-pushed the feat/add-patchset-download-cli-api branch from fa735b0 to b72e399 Compare October 9, 2020 22:20

lukasheinrich approved these changes Oct 10, 2020

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lukasheinrich merged commit 6ce4669 into master Oct 10, 2020

lukasheinrich deleted the feat/add-patchset-download-cli-api branch October 10, 2020 06:35

matthewfeickert added a commit that referenced this pull request Oct 13, 2020

fix: Remove improper defaults for contrib download (#1105)

e1e6cd5

* Remove contrib download defaults for arguments ARCHIVE_URL OUTPUT_DIRECTORY * Amends PR #1046

matthewfeickert mentioned this pull request Oct 15, 2020

move cli/contrib.py to contrib/cli.py #1117

Closed

matthewfeickert mentioned this pull request Dec 6, 2020

Revise tests that rely on importlib.reload #1205

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matthewfeickert mentioned this pull request Jun 9, 2021

test_patchset_download failing in CI due to download of gzip file failing #1485

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feat: Add API to download likelihood patchset archives #1046

feat: Add API to download likelihood patchset archives #1046

matthewfeickert commented Aug 22, 2020 •

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kratsg commented Sep 15, 2020

		# hide
		CACHE_MODULE, sys.modules[module_name] = sys.modules[module_name], None

feat: Add API to download likelihood patchset archives #1046

feat: Add API to download likelihood patchset archives #1046

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matthewfeickert commented Aug 22, 2020 • edited

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