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Merge pull request #343 from dpryan79/blacklist_lint
Have linting obey blacklist, modify bioconductor skeleton, fix cleaning of CRAN recipes
2 parents f4e5940 + 0ff4edc commit 165b55d

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6 files changed

+14
-11
lines changed

6 files changed

+14
-11
lines changed

bioconda_utils/bioconda_utils-requirements.txt

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@ anaconda-client=1.6.*
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argh=0.26.*
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beautifulsoup4=4.6.*
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conda=4.5.11
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conda-build=3.14.4
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conda-build=3.15.1
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galaxy-lib>=18.9.1
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jinja2=2.10.*
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jsonschema=2.6.*

bioconda_utils/bioconductor_skeleton.py

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -763,7 +763,6 @@ def sub_placeholders(x):
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),
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(
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'source', OrderedDict((
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('fn', '{{ name }}_{{ version }}.tar.gz'),
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('url', url),
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('sha256', self.sha256),
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)),

bioconda_utils/cli.py

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -48,14 +48,15 @@ def select_recipes(packages, git_range, recipe_folder, config_filename, config,
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selected_recipes = list(utils.get_recipes(recipe_folder, packages))
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_recipes = []
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for recipe in selected_recipes:
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if recipe in blacklisted_recipes and recipe in changed_recipes:
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stripped = os.path.relpath(recipe, recipe_folder)
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if stripped in blacklisted_recipes and recipe in changed_recipes:
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logger.warning('%s is blacklisted but also has changed. Consider '
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'removing from blacklist if you want to build it', recipe)
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if force:
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_recipes.append(recipe)
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logger.debug('forced: %s', recipe)
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continue
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if recipe in blacklisted_recipes:
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if stripped in blacklisted_recipes:
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logger.debug('blacklisted: %s', recipe)
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continue
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if git_range:

bioconda_utils/cran_skeleton.py

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Original file line numberDiff line numberDiff line change
@@ -144,6 +144,9 @@ def clean_yaml_file(package, no_windows):
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# Remove file license
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lines = filter_lines_regex(lines, r' [+|] file LICEN[SC]E', '')
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# Remove file name lines, which aren't needed as of conda-build3
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lines = filter_lines_regex(lines, r'^\s+fn:\s*.*$', '')
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# Replace GPL2 or GPL3 string created by conda skeleton cran with long
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# format
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lines = filter_lines_regex(lines, gpl2_short, gpl2_long)

bioconda_utils/maintainers.yaml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
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extra:
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recipe-maintainers:
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recipe-maintainers:
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- MathiasHaudgaard
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- FrodePedersen
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- ArneKr

test/test_utils.py

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -651,27 +651,27 @@ def test_skip_dependencies():
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one:
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meta.yaml: |
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package:
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name: one
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name: skip_dependencies_one
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version: 0.1
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two:
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meta.yaml: |
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package:
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name: two
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name: skip_dependencies_two
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version: 0.1
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requirements:
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build:
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- one
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- skip_dependencies_one
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- nonexistent
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three:
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meta.yaml: |
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package:
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name: three
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name: skip_dependencies_three
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version: 0.1
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requirements:
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build:
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- one
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- skip_dependencies_one
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run:
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- two
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- skip_dependencies_two
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""", from_string=True)
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r.write_recipes()
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pkgs = {}

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