Code

Migrate to conda-build 3.#293

Code

Merged

johanneskoester merged 127 commits intomasterbioconda/bioconda-utils:masterfrom cb3-migrationbioconda/bioconda-utils:cb3-migrationCopy head branch name to clipboardJul 19, 2018

+2,760-1,926

Commits

Commits on Apr 23, 2018

• Pin to conda-build 3.

  johanneskoester

  committed
  a6e402a

• Depend on latest conda-forge-pinning package.

  Show description for 12f128e
  johanneskoester

  committed
  12f128e

• Try downgrading to last minor release of conda.

  johanneskoester

  committed
  66c1a4c

• Try using conda 4.3.

  johanneskoester

  committed
  9d6636c

• Try 4.5.0

  johanneskoester

  committed
  6ee9510

• Handle UnableToParse

  johanneskoester

  committed
  63f809f

Commits on Apr 24, 2018

• Remove galaxy-lib version restriction.

  johanneskoester

  committed
  3664db1

• adapt to conda 4.5

  johanneskoester

  committed
  20d58eb

• use get_output_file_paths instead of get_output_file_path

  johanneskoester

  committed
  14aafd2

• Merge branch 'cb3-migration' of github.com:bioconda/bioconda-utils into cb3-migration

  johanneskoester

  committed
  76035ea

• Merge branch 'master' into cb3-migration

  johanneskoester

  committed
  c847294

• Add lint for deprecated numpy spec.

  johanneskoester

  committed
  f6b5669

• Document new lint.

  johanneskoester

  committed
  0d7d1cc

• register lint.

  johanneskoester

  committed
  55e1e14

• fix tests

  johanneskoester

  committed
  82abcf7

• fix lint

  johanneskoester

  committed
  3384875

• adapt test cases and remove obsolete ones.

  johanneskoester

  committed
  38aaf26

Commits on Apr 25, 2018

• Remove env_matrix.

  johanneskoester

  committed
  07eb371

• fix typo

  johanneskoester

  committed
  de2e4a2

• fixes and further cleanup

  johanneskoester

  committed
  6014495

• fixes

  johanneskoester

  committed
  9a4a3d9

• Fixes.

  johanneskoester

  committed
  312f982

Commits on Apr 26, 2018

• fix typo

  johanneskoester

  committed
  06fa571

• fixes

  johanneskoester

  committed
  742e61d

• fixes

  johanneskoester

  committed
  2aaf71e

• fixes.

  johanneskoester

  committed
  d888281

• fix DAG

  johanneskoester

  committed
  7d97668

• Linting now uses fully rendered recipes, and checks all combinations of the variant matrix and both linux and osx.

  johanneskoester

  committed
  be141e0

• fix conda execution in docker

  johanneskoester

  committed
  660dc84

• fix argument

  johanneskoester

  committed
  b3e2eda

• fixes.

  johanneskoester

  committed
  7934506

Commits on Apr 30, 2018

• Adapt numpy x.x lint to new multi-metadata strategy.

  johanneskoester

  committed
  a2aa8e1

• properly render metadata when finding built package paths.

  johanneskoester

  committed
  26132ed

• fixes.

  johanneskoester

  committed
  7aa4a7c

• fixes

  johanneskoester

  committed
  69b0123

Commits on May 1, 2018

• fix test for rendering sandboxing

  daler

  committed
  2102ad0

• disable skip-existing

  daler

  committed
  ff204fe

Commits on May 2, 2018

• Use same build args for the copying as for building.

  johanneskoester

  committed
  3e1533a

Commits on May 4, 2018

• add test for conda-forge pinning

  daler

  committed
  3cd0ff6

Commits on May 5, 2018

• add ability to have separate bioconda pins

  daler

  committed
  c6ed119

• pep8

  daler

  committed
  31bd484

• add some more docs on testing

  daler

  committed
  8139e77

• add bioconda conda_build_config.yaml

  daler

  committed
  788f6d5

• add first metadata fix

  daler

  committed
  cfa4060

• update tests for load_first_metadata

  daler

  committed
  04543f3

• first pass of cb3 migration docs

  daler

  committed
  526e48d

• port bioconductor_skeleton to use cb3 compilers; improve detection

  daler

  committed
  ed371bd

• update bioconductor_skeleton test

  daler

  committed
  9473f74

• more cb3 docs

  daler

  committed
  02e89ae

• add anaconda to channels

  daler

  committed
  3f57264

• add anaconda channel to circleci setup

  daler

  committed
  4494c42

• short-circuit filtering if skipped

  daler

  committed
  2b97c0b

• fix text to only check names

  daler

  committed
  0969bce

• add test for when CI=true

  daler

  committed
  a3441ea

Commits on May 6, 2018

• add extra checks that built pkgs exist

  daler

  committed
  a704232

• add test for cb3 outputs

  daler

  committed
  2da3a20

• clean up cb3 output test; typos

  daler

  committed
  08562bf

• utils.Progress: remove unnecessary sleep

  mbargull

  committed
  9a3a9d8

• pkg_test: use --involucro-path to prevent download in galaxy-lib

  mbargull

  committed
  6a86254

Commits on May 7, 2018

• remove anaconda channel

  daler

  committed
  71f52fa

• simplify htslib in test

  daler

  committed
  7999eec

• add compiler test

  daler

  committed
  71b6b0c

• fix htslib max pin

  daler

  committed
  ce67dff

• update docs to reflect run_exports

  daler

  committed
  d6ea7a1

• Merge branch 'master' into cb3-migration

  daler

  authored
  b2c82d9

Commits on May 8, 2018

• Update cb3.rst

  kyleabeauchamp

  authored
  d374363

Commits on May 9, 2018

• Merge pull request #297 from kyleabeauchamp/patch-1

  Show description for 232e160
  daler

  authored
  232e160

Commits on May 13, 2018

• Merge branch 'master' into cb3-migration

  johanneskoester

  authored
  ea608fb

• update docs

  daler

  committed
  c9ec48b

• add lint functions for compilers and fn

  daler

  committed
  fd7bfee

• add linting docs

  daler

  committed
  3ec7681

• bring back the noarch lint docs

  daler

  committed
  80d25c7

Commits on May 16, 2018

• render with finalize=False where possible

  mbargull

  committed
  7079bb3

• rename load_conda_config to load_conda_build_config

  mbargull

  committed
  0ae67ab

• use conda.exports (public API)

  mbargull

  committed
  884e757

• pin conda-forge-pinning, update conda/conda-build pins

  mbargull

  committed
  91639b8

• lint: handle if source is a list

  mbargull

  committed
  77b4f84

• adjust tests

  mbargull

  committed
  7002683

• show test durations

  mbargull

  committed
  a089bd0

• lint: use decorator instead explicit loops

  mbargull

  committed
  b6121dc

• lint: fix decorator, pass through __name__ for registry

  mbargull

  committed
  8f026ad

• lint: fix decorator, pass through __name__ for registry (2)

  mbargull

  committed
  933a954

• run long-running tests separately

  mbargull

  committed
  03960fe

Commits on May 22, 2018

• Merge branch 'master' into cb3-migration

  johanneskoester

  authored
  4686605

Commits on May 25, 2018

• docker_utils: use base image acc. to BIOCONDA_UTILS_TAG

  mbargull

  committed
  b122120

• Remove a priori filtering. Instead filter when each recipe is considered.

  johanneskoester

  committed
  b738ca5

• Naming.

  johanneskoester

  committed
  5ea1d5e

• Skip filter tests for now.

  johanneskoester

  committed
  325f0f2

• Disable DAG generation.

  johanneskoester

  committed
  d3530ad

• Activate DAG calculation again (we cannot avoid it because we need the topological sorting).

  johanneskoester

  committed
  26ec23c

• Fast loading of metadata for DAG.

  johanneskoester

  committed
  668ec38

Commits on May 26, 2018

• Only use host dependencies when building DAG.

  johanneskoester

  committed
  a6dabe3

• get_package_paths returns tuple

  daler

  committed
  2fb47ea

• utils.get_package_paths: only return paths

  mbargull

  committed
  6072d39

• requirements: update conda, conda-build, conda-forge-pinning

  mbargull

  committed
  62f1d52

• use bypass_env_check=True when we use non-finalized renderings

  mbargull

  committed
  9821159

• requirements: use conda-build=3.10.3 for now

  mbargull

  committed
  62efbd5

• test_utils: disable the remaining filter_recipes test

  mbargull

  committed
  66497f2

Commits on May 29, 2018

• Abort building if build strings in repo are divergent

  mbargull

  committed
  c074b13

• fix previous commit: add Python's redundant colon

  mbargull

  committed
  4085e6a

• fix generate_docs.py

  mbargull

  committed
  b002ec0

• fix another typo

  mbargull

  committed
  b4917aa

Commits on Jun 2, 2018

• support linting just before building

  daler

  committed
  69a1f35

• sort recipes for linting

  daler

  committed
  ec47a17

• better noarch detection

  daler

  committed
  77d673b

• Merge branch 'cb3-migration' of github.com:bioconda/bioconda-utils into cb3-migration

  daler

  committed
  7a0c70b

• default df

  daler

  committed
  0302291

• be clear which recipe the problem is on

  daler

  committed
  7d35d0b

• add back in debug info on linting

  daler

  committed
  b2fb765

• more generic check for compilers

  daler

  committed
  b6763c5

Commits on Jun 3, 2018

• add conda_build_config files consistently

  mbargull

  committed
  41f39c0

• fix previous commit

  mbargull

  committed
  e0603ec

• fix previous commit again

  mbargull

  committed
  190ff4f

Commits on Jun 14, 2018

• fix mulled upload: iterate over all generated images.

  johanneskoester

  committed
  9fdbc8f

Commits on Jun 19, 2018

• build: fix collecting mulled_images

  mbargull

  committed
  6c45c87

Commits on Jun 22, 2018

• requirements: require python >=3.6

  mbargull

  committed
  3ab8023

Commits on Jun 23, 2018

• build: skip builds early based on num of existing builds in channel

  mbargull

  committed
  d4701c6

Commits on Jun 24, 2018

• build: topo-sort connected components before merging

  mbargull

  committed
  99782c2

• docs: handle extra.notes being a list

  mbargull

  committed
  e033e47

• build: handle UnsatisfiableError

  mbargull

  committed
  44565d0

• fix import

  mbargull

  committed
  86fc487

Commits on Jun 26, 2018

• [WIP] update to conda-build 3.10.9 (#312)

  Show description for 4f6b405
  

  mbargull

  authored and

  johanneskoester

  committed
  4f6b405

Commits on Jul 2, 2018

• Add paper to the homepage.

  johanneskoester

  committed
  4e35af8

Commits on Jul 4, 2018

• Handle dependency cycles (#313)

  Show description for b0df159
  

  mbargull

  authored and

  johanneskoester

  committed
  b0df159

Commits on Jul 18, 2018

• requirements: update to conda-forge-pinning 2018.07.18

  mbargull

  committed
  5800ebe

• Merge pull request #315 from bioconda/cf-pinning-2018-07-18

  Show description for 9349490
  bgruening

  authored
  9349490

Commits on Jul 19, 2018

• Merge branch 'master' into cb3-migration

  johanneskoester

  authored
  9e40c85