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conda-forge Repodata Patching

What is a repodata patch?

Sometimes, already published conda packages contain metadata errors (which can be repaired without needing to rebuild the packages). Most commonly, package dependencies are incorrect, but the package artifacts themselves are fine. A repodata patch specifies which packages are contain errors and how the package should be modified to fix the error.

The best way to make a new patch is to use the patch YAML specification below. Custom patches in python can be put into the gen_patch_json.py file.

Repodata patch YAML specification

The files in this directory are used to construct repodata patches for conda-forge. Typically, a single feedstock will have a single YAML file specifying the patches for the packages produced by that feedstock. Use comments liberally to describe why the patch exists.

Patches are specified by two main blocks.

  • The if block specifies a set of conditions under which the changes in the then block are applied.
  • The different conditions in the if block are combined with a logical AND.
  • Any condition may be prefixed by not_ and will be negated.
  • The if conditions can use shell glob syntax as implemented in the python fnmatch module in the standard library. The optional "?( *)" pattern from extended glob syntax is allowed to match zero or one sequences of spaces plus any other characters.
  • The then section uses the Python string.Template system to allow the version, build_number, name, or subdir values to be inserted into strings via templates (e.g., "blah <=${version}") at runtime.
  • Multiple patches can be in the same file using separate YAML documents (i.e., separate the data by --- on a new line).
if:
  # possible conditions
  # list of subdirs or a single subdir (e.g., "linux-64")
  subdir_in: linux-64
  # any subdir but linux-64
  not_subdir_in: linux-64

  # list of artifact names or a single name (e.g., "ngmix-2.3.0-py38h50d1736_1.conda")
  artifact_in: ngmix-2.3.0-py38h50d1736_1.conda

  # any key in the repodata entry (e.g., "version" or "build_number") with an operation
  <repodata key>_<ge, gt, le, lt>: <value>
  # this means version > 1.0.0
  version_gt: 1.0.0
  # keeps any record with timestamp < value
  # you can generate the current time via
  #  python -c "import time; print(f'{time.time():.0f}000')"
  timestamp_lt: 1633470721000

  # any key in the repodata entry (e.g., "version" or "build_number") and a list of values or single value
  <repodata key>_in: <list or single item>

  # this means the build number is in the set {0, 1, 2}
  build_number_in: [0, 1, 2]

  # has specific dependencies as either a list or a single string
  has_depends: numpy*  # matches 'numpy', 'nump-blah', or 'numpy 5.6'
  has_depends: numpy?( *)  # matches 'numpy' or 'numpy 5.6' but not 'numpy-blah'
  has_depends: numpy  # matches "numpy" exactly (i.e., no pins)

  # has specific constraints as either a list or a single key
  has_constrains: numpy*  # matches 'numpy', 'nump-blah', or 'numpy 5.6'
  has_constrains: numpy?( *)  # matches 'numpy' or 'numpy 5.6' but not 'numpy-blah'
  has_constrains: numpy  # matches "numpy" exactly (i.e., no pins)

  # single value for a key that should match
  <repodata key>: <value>
  version: 1.0.0
then:
  # list of instructions to change things

  # add to the depends or constrains section of the repodata
  # this function will not add items already present in the record
  - add_<depends or constrains>: <list of str or single str>
  # you can use data from the record being patched like this
  # only name, version, build_number and subdir are supported
  - add_depends: mypackage <=${version}

  # remove from the depends or constrains sections of the repodata
  - remove_<depends or constrains>: <list of str or single str>

  # remove entries from track_features
  - remove_track_features: <list of str or str>

  # add entries to track_features
  - add_track_features: <list of str or str>

  # reset the depends or constrains section of the repodata
  # this function resets the depends or constrains to the specified value(s)
  - reset_<depends or constrains>: <list of str or single str>
  # you can use data from the record being patched like this
  # only name, version, build_number and subdir are supported
  - reset_depends: mypackage <=${version}

  # replace entries via an exact match in either the depends or constrains sections
  - replace_<depends or constrains>:
      # str of thing to be replaced
      old: matplotlib ==1.3.0
      # thing to replace `old` with
      new: matplotlib-base ==1.4.0
  # globs are allowed in the "old" field so * needs to be escaped via [*]
  - replace_<depends or constrains>:
      # str of thing to be replaced
      old: matplotlib 1.3.[*]  # matches matplotlib 1.3.* exactly
      # thing to replace `old` with
      new: matplotlib-base ==1.4.0
  - replace_<depends or constrains>:
      # str of thing to be replaced
      old: matplotlib 1.3.*  # matches matplotlib 1.3.0, matplotlib 1.3, etc.
      # thing to replace `old` with
      new: matplotlib-base ==1.4.0
  - replace_<depends or constrains>:
      # str of thing to be replaced
      old: matplotlib ==1.3.0
      # thing to replace `old` with
      new: ${old},<1.4.0  # you can refer to the "old" value as well

  # rename a dependency - this preserves the version information and simply renames the package
  - rename_depends:
      # str of thing to be renamed
      old: matplotlib
      # new name for thing
      new: matplotlib-base

  # relax an exact pin (e.g., blah ==1.0.0) to something like blah >=1.0.0 and possibly with
  # `,<2.0a0` added if max_pin='x'
  - relax_exact_depends:
      # the package name whose constraint should be relaxed
      name: matplotlib
      # optional string of 'x', 'x.x' etc. format specify an upper bound
      # if not given, no upper bound is applied
      # max_pin: 'x.x'

  # make a dependency version constraint stricter
  - tighten_depends:
      # package to pin stricter
      name: matplotlib  # this field can use the fnmatch glob syntax
      # you must give one of max_pin or upper_bound
      # optional way to specify the new maximum pin as 'x', 'x.x', etc.
      max_pin: 'x.x'
      # optional way to specify upper bound explicitly
      # do not use with `max_pin`
      upper_bound: 2.0.1

  # make a dependency version constraint looser
  - loosen_depends:
      # package to pin looser
      name: matplotlib  # this field can use the fnmatch glob syntax
      # you must give one of max_pin or upper_bound
      # optional pinning expression 'x', 'x.x', etc. to set how much looser to make the pin
      max_pin: 'x.x'
      # optional way to specify upper bound explicitly
      # do not use with `max_pin`
      upper_bound: 2.0.1
---
# more than one patch can be in the file by putting the next one here as a new YAML doc
if:
  ...
then:
  ...
---
if:
  ...
then:
  ...

Warning

The condition timestamp_lt is required to prevent your patch from modifying any packages built in the future. Don't forget to calculate it with python -c "import time; print(f'{time.time():.0f}000')" and include it in the if: section of your patch

Testing New Patches using show_diff.py

Tip

You can install a development environment for testing your repodata patch using the environment file dev-env-for-patches.yaml

The show_diff.py script in this directory can be used to test out modifications to gen_patch_json.py. This scripts shows the difference between the package records currently available on anaconda.org/conda-forge and those produced from the patch instructions produced by gen_patch_json.py.

Usage is:

usage: show_diff.py [-h] [--subdirs [SUBDIRS [SUBDIRS ...]]] [--use-cache]

show repodata changes from the current gen_patch_json

optional arguments:
  -h, --help            show this help message and exit
  --subdirs [SUBDIRS [SUBDIRS ...]]
                        subdir(s) show, default is all
  --use-cache           use cached repodata files, rather than downloading
                        them

Repodata is cached in a cache directory in the current directory or in the path specified by the CACHE_DIR environment variable.

Typically, show_diff.py is run without any argument to download the necessary repodata followed by repeated calls to show_diff.py --use-cache to test out changes to the gen_patch_json.py script.

Tip

If you're having trouble running show_diff.py locally, don't despair. You should still submit your patch. The Azure job also returns this information. Search the build log for patching repodata: and copy-paste the output for all the architectures to your Pull Request. Stop copying once you've reached patching repodata: 100%

Patch JSON Format for anaconda.org

This scheme generates one file per subdir, patch_instructions.json. This file has entries

instructions = {
        "patch_instructions_version": 1,
        "packages": defaultdict(dict),
        "revoke": [],
        "remove": [],
    }

remove are lists of filenames that will not show up in the index but may still be downloadable with a direct URL to the file.

packages is a dictionary, where keys are package filenames. Values are dictionaries similar to the contents of each package in repodata.json. Any values provided in packages here overwrite the values in repodata.json. Any value set to None is removed.

A tool downloads this package when it sees updates to it, and applies the patch_instructions.json to the repodata of the conda-forge channel on anaconda.org