update to conda-build 3.10.9 #312
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johanneskoester
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Jun 26, 2018
johanneskoester
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* Pin to conda-build 3. * Depend on latest conda-forge-pinning package. This will ensure that conda-build 3 is always using the pinnings defined in https://github.com/conda-forge/conda-forge-pinning-feedstock/blob/master/recipe/conda_build_config.yaml By contributing to this list, we can maintain compatibility with conda-forge. * Try downgrading to last minor release of conda. * Try using conda 4.3. * Try 4.5.0 * Handle UnableToParse * Remove galaxy-lib version restriction. * adapt to conda 4.5 * use get_output_file_paths instead of get_output_file_path * Add lint for deprecated numpy spec. * Document new lint. * register lint. * fix tests * fix lint * adapt test cases and remove obsolete ones. * Remove env_matrix. * fix typo * fixes and further cleanup * fixes * Fixes. * fix typo * fixes * fixes * fixes. * fix DAG * Linting now uses fully rendered recipes, and checks all combinations of the variant matrix and both linux and osx. * fix conda execution in docker * fix argument * fixes. * Adapt numpy x.x lint to new multi-metadata strategy. * properly render metadata when finding built package paths. * fixes. * fixes * fix test for rendering sandboxing * disable skip-existing * Use same build args for the copying as for building. * add test for conda-forge pinning * add ability to have separate bioconda pins * pep8 * add some more docs on testing * add bioconda conda_build_config.yaml * add first metadata fix * update tests for load_first_metadata * first pass of cb3 migration docs * port bioconductor_skeleton to use cb3 compilers; improve detection * update bioconductor_skeleton test * more cb3 docs * add anaconda to channels * add anaconda channel to circleci setup * short-circuit filtering if skipped * fix text to only check names * add test for when CI=true * add extra checks that built pkgs exist * add test for cb3 outputs * clean up cb3 output test; typos * utils.Progress: remove unnecessary sleep * pkg_test: use --involucro-path to prevent download in galaxy-lib * remove anaconda channel * simplify htslib in test * add compiler test * fix htslib max pin * update docs to reflect run_exports * Update cb3.rst * update docs * add lint functions for compilers and fn * add linting docs * bring back the noarch lint docs * render with finalize=False where possible * rename load_conda_config to load_conda_build_config * use conda.exports (public API) * pin conda-forge-pinning, update conda/conda-build pins * lint: handle if source is a list * adjust tests * show test durations * lint: use decorator instead explicit loops * lint: fix decorator, pass through __name__ for registry * lint: fix decorator, pass through __name__ for registry (2) * run long-running tests separately * docker_utils: use base image acc. to BIOCONDA_UTILS_TAG * Remove a priori filtering. Instead filter when each recipe is considered. * Naming. * Skip filter tests for now. * Disable DAG generation. * Activate DAG calculation again (we cannot avoid it because we need the topological sorting). * Fast loading of metadata for DAG. * Only use host dependencies when building DAG. * get_package_paths returns tuple * utils.get_package_paths: only return paths * requirements: update conda, conda-build, conda-forge-pinning * use bypass_env_check=True when we use non-finalized renderings * requirements: use conda-build=3.10.3 for now * test_utils: disable the remaining filter_recipes test * Abort building if build strings in repo are divergent * fix previous commit: add Python's redundant colon * fix generate_docs.py * fix another typo * support linting just before building * sort recipes for linting * better noarch detection * default df * be clear which recipe the problem is on * add back in debug info on linting * more generic check for compilers * add conda_build_config files consistently * fix previous commit * fix previous commit again * fix mulled upload: iterate over all generated images. * build: fix collecting mulled_images * requirements: require python >=3.6 * build: skip builds early based on num of existing builds in channel * build: topo-sort connected components before merging * docs: handle extra.notes being a list * build: handle UnsatisfiableError * fix import * [WIP] update to conda-build 3.10.9 (#312) * build: rename --prelint to --lint, add --lint-only/--lint-exclude args * requirements: update to conda-build 3.10.9 * build: remove default value for --lint-exclude * requirements: require python >=3.6 * meta.get_section might return None (conda-build 3.10.9 compat) * silence most flake8 nagging * bioconductor: fix missing newline at EOF for post-link.sh * fix typo * use meta.get_value preferably * make flake8 shut up already * meta.get_value only works for path with depth 2 * lint: fix should_not_be_noarch for conda_build >3.10.3 * lint._has_compilers: also check for old compiler packages * lint._get_deps: fix sections being unset on default * docs: use only one job for debugging * Add paper to the homepage. * Handle dependency cycles (#313) * fix minor bug in `build --lint-exclude` * utils.check_recipe_skippable: avoid additional FILTER msg if nothing to do * utils.get_dag: 'dep' can be empty string for unevaluated jinja expressions * utils.get_dag: respect dependencies from build and run environments * build.build_recipes: gracefully handle(=skip) packages in dependency cycles * requirements: update to conda-forge-pinning 2018.07.18
johanneskoester
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that referenced
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Jul 20, 2018
* Pin to conda-build 3. * Depend on latest conda-forge-pinning package. This will ensure that conda-build 3 is always using the pinnings defined in https://github.com/conda-forge/conda-forge-pinning-feedstock/blob/master/recipe/conda_build_config.yaml By contributing to this list, we can maintain compatibility with conda-forge. * Try downgrading to last minor release of conda. * Try using conda 4.3. * Try 4.5.0 * Handle UnableToParse * Remove galaxy-lib version restriction. * adapt to conda 4.5 * use get_output_file_paths instead of get_output_file_path * Add lint for deprecated numpy spec. * Document new lint. * register lint. * fix tests * fix lint * adapt test cases and remove obsolete ones. * Remove env_matrix. * fix typo * fixes and further cleanup * fixes * Fixes. * fix typo * fixes * fixes * fixes. * fix DAG * Linting now uses fully rendered recipes, and checks all combinations of the variant matrix and both linux and osx. * fix conda execution in docker * fix argument * fixes. * Adapt numpy x.x lint to new multi-metadata strategy. * properly render metadata when finding built package paths. * fixes. * fixes * fix test for rendering sandboxing * disable skip-existing * Use same build args for the copying as for building. * add test for conda-forge pinning * add ability to have separate bioconda pins * pep8 * add some more docs on testing * add bioconda conda_build_config.yaml * add first metadata fix * update tests for load_first_metadata * first pass of cb3 migration docs * port bioconductor_skeleton to use cb3 compilers; improve detection * update bioconductor_skeleton test * more cb3 docs * add anaconda to channels * add anaconda channel to circleci setup * short-circuit filtering if skipped * fix text to only check names * add test for when CI=true * add extra checks that built pkgs exist * add test for cb3 outputs * clean up cb3 output test; typos * utils.Progress: remove unnecessary sleep * pkg_test: use --involucro-path to prevent download in galaxy-lib * remove anaconda channel * simplify htslib in test * add compiler test * fix htslib max pin * update docs to reflect run_exports * Update cb3.rst * update docs * add lint functions for compilers and fn * add linting docs * bring back the noarch lint docs * render with finalize=False where possible * rename load_conda_config to load_conda_build_config * use conda.exports (public API) * pin conda-forge-pinning, update conda/conda-build pins * lint: handle if source is a list * adjust tests * show test durations * lint: use decorator instead explicit loops * lint: fix decorator, pass through __name__ for registry * lint: fix decorator, pass through __name__ for registry (2) * run long-running tests separately * docker_utils: use base image acc. to BIOCONDA_UTILS_TAG * Remove a priori filtering. Instead filter when each recipe is considered. * Naming. * Skip filter tests for now. * Disable DAG generation. * Activate DAG calculation again (we cannot avoid it because we need the topological sorting). * Fast loading of metadata for DAG. * Only use host dependencies when building DAG. * get_package_paths returns tuple * utils.get_package_paths: only return paths * requirements: update conda, conda-build, conda-forge-pinning * use bypass_env_check=True when we use non-finalized renderings * requirements: use conda-build=3.10.3 for now * test_utils: disable the remaining filter_recipes test * Abort building if build strings in repo are divergent * fix previous commit: add Python's redundant colon * fix generate_docs.py * fix another typo * support linting just before building * sort recipes for linting * better noarch detection * default df * be clear which recipe the problem is on * add back in debug info on linting * more generic check for compilers * add conda_build_config files consistently * fix previous commit * fix previous commit again * fix mulled upload: iterate over all generated images. * build: fix collecting mulled_images * requirements: require python >=3.6 * build: skip builds early based on num of existing builds in channel * build: topo-sort connected components before merging * docs: handle extra.notes being a list * build: handle UnsatisfiableError * fix import * [WIP] update to conda-build 3.10.9 (#312) * build: rename --prelint to --lint, add --lint-only/--lint-exclude args * requirements: update to conda-build 3.10.9 * build: remove default value for --lint-exclude * requirements: require python >=3.6 * meta.get_section might return None (conda-build 3.10.9 compat) * silence most flake8 nagging * bioconductor: fix missing newline at EOF for post-link.sh * fix typo * use meta.get_value preferably * make flake8 shut up already * meta.get_value only works for path with depth 2 * lint: fix should_not_be_noarch for conda_build >3.10.3 * lint._has_compilers: also check for old compiler packages * lint._get_deps: fix sections being unset on default * docs: use only one job for debugging * Add nested recipe check to get_recipes Currently get_recipes only support recipes nested up to two deep from the recipe_folder provided. Our application of get_recipes, and potential future uses from others, has recipes nested deeper. This purposed implementation will provide the ability to locate all recipes, no matter how deep, within the user provided recipe_folder. * Add test for new get_recipes deep nesting check get_recipes was changed to allow for different levels of recipe nesting. test_depthcheck_get_recipe() will test get_recipes ability to find different levels of nested recipes. * Update test_utils.py * update test_depthcheck_get_recipe * update test_depthcheck_get_recipe * Update test_utils.py * Update test_utils.py * Update test_utils.py * update test_depthcheck_get_recipe * Re-test with circle ci * Update utils.py * Update test_utils.py * Update test_utils.py * Update test_utils.py * Update utils.py
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(based on gh-311)
Trying out
conda-build 3.10.9which includes a couple of linting speedups (such that a full linting job should be fast again -- only one remaining speedup issue is remains; see that issue for run time numbers).Probably requires some compatibility fixes.