Remove mamba support

.github/workflows/deploy.yml

@@ -19,11 +19,13 @@ jobs:
           auto-update-conda: true
           auto-activate-base: true
           activate-environment: ""
+          channel-priority: strict
+          miniforge-variant: Miniforge3
       - name: linux conda build and upload
         shell: bash -l {0}
         env:
           ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
         run: |
-          conda install -n base -c conda-forge conda-build mamba boa anaconda-client -y
+          conda install -n base -c conda-forge conda-build anaconda-client -y
           conda config --set anaconda_upload yes
-          conda mambabuild -c conda-forge --user ilastik-forge conda-recipe
+          conda build -c conda-forge --user ilastik-forge conda-recipe

.github/workflows/test.yml

@@ -19,20 +19,22 @@ jobs:
           auto-update-conda: true
           auto-activate-base: true
           activate-environment: ""
+          channel-priority: strict
+          miniforge-variant: Miniforge3
       - name: install common dependencies
-        run: conda install -n base -c conda-forge -c nodefaults conda-build mamba boa -y
+        run: conda install -n base -c conda-forge -c nodefaults conda-build -y
       - name: linux conda build test
         if: matrix.os == 'ubuntu-latest'
         shell: bash -l {0}
-        run: conda mambabuild -c conda-forge conda-recipe
+        run: conda build -c conda-forge conda-recipe
       - name: osx test
         if: matrix.os == 'macos-latest'
         shell: bash -l {0}
-        run:  conda mambabuild -c conda-forge conda-recipe
+        run:  conda build -c conda-forge conda-recipe
       - name: windows conda-build
         if: matrix.os == 'windows-latest'
         shell: cmd /C CALL {0}
-        run: conda mambabuild -c conda-forge conda-recipe
+        run: conda build -c conda-forge conda-recipe
         # HACK: due to a bug in conda-build need to point to
         # libarchive explicitly.
         # https://github.com/conda/conda/issues/12563#issuecomment-1494264704

README.md

@@ -45,8 +45,8 @@ Run `conda install anaconda-client`. You need to be logged in to your https://an
 ```yaml
 # common configuration for all packages defined in shared-config:
 shared-config:
-  # backend: new in 0.4, added support for `conda` and `mamba` with `conda` being the default
-  backend: mamba
+  # backend: new in 0.4, only supports `conda` since removal of mamba support
+  backend: conda
   # will translate to --python for every conda-build, deprecated, use pin-file
   python: '3.6'
   # will translate to --numpy for every conda-build, deprecated, use pin-file
@@ -61,6 +61,9 @@ shared-config:
     - conda-forge
   # channel to upload recipes to
   destination-channel: my-personal-channel
+
+  # Choose which package type(s) are outputted. (Accepted inputs .tar.bz2 or 1, .conda or 2)
+  package-format: .conda                      
 ```
 
 #### Package definitions
@@ -119,3 +122,11 @@ MACOSX_DEPLOYMENT_TARGET=10.9 publish-conda-stack my-recipe-specs.yaml
 ```
 
 The `build-recipes.py` script parses the packages from `my-recipe-specs.yaml`, and for each package checks whether an up-to-date version is already available on the `destination-channel` listed in `my-recipe-specs.yaml`.  If the packages don't yet exist in that channel set, it will build the package and upload it.
+
+
+### Changelog
+
+#### 0.6.0
+
+* Added shared config key `package-format` which can be ``.tar.bz2` or `1`, `.conda` or `2`.
+  Default is ``.conda`.

conda-recipe/meta.yaml

@@ -41,7 +41,7 @@ test:
     - pytest
     - pytest-mock
   commands:
-    - pytest --doctest-modules .
+    - pytest
 
 about:
   home: https://github.com/ilastik/publish-conda-stack

dev/README.md

@@ -3,10 +3,10 @@
 ## Create a development environment
 
 ```bash
-mamba env create --name pcs-dev --file dev/environment-dev.yml
+conda env create --name pcs-dev --file dev/environment-dev.yml
 ```
 
-This will create an environment with the name `pcs-dev`, that can be activated with `mamba activate pcs-dev`.
+This will create an environment with the name `pcs-dev`, that can be activated with `conda activate pcs-dev`.
 
 ## Automatic versioning with bumpversion
 

dev/environment-dev.yml

@@ -2,12 +2,11 @@ channels:
   - conda-forge
 dependencies:
   - anaconda-client
+  - argcomplete
   - black
-  - boa
   - bumpversion
-  - conda-build
+  - conda-build >=24.11.0
   - conda-verify
-  - mamba
   - mypy
   - pre_commit
   - pytest

pyproject.toml

@@ -1,2 +1,6 @@
 [tool.isort]
 profile = "black"
+
+[tool.pytest.ini_options]
+addopts = "--doctest-modules"
+

setup.py

@@ -15,7 +15,7 @@
     install_requires=[
         "anaconda-client",
         "argcomplete",
-        "conda-build>=3.18.10",
+        "conda-build>=24.11.0",
         "ruamel.yaml>=0.15.2",
     ],
     entry_points={

src/publish_conda_stack/cmdutil.py

@@ -7,31 +7,27 @@
 
 
 class CondaCommand(IntEnum):
-    RENDER: int = auto()
-    SEARCH: int = auto()
-    BUILD: int = auto()
+    RENDER = auto()
+    SEARCH = auto()
+    BUILD = auto()
 
 
 def conda_cmd_base(command: CondaCommand, shared_config: dict) -> List[str]:
     variant_config = shared_config.get("master-conda-build-config", None)
     variant_args = ["-m", variant_config] if variant_config else []
 
-    # render is not supported in mamba, here we must use conda
+    backend = shared_config.get("backend", DEFAULT_BACKEND)
+    if backend not in ["conda"]:
+        raise ValueError(f"Unknown backend: {backend}. Only `conda` is supported.")
+
+    args = [backend]
+
     if command == CondaCommand.RENDER:
-        args = ["conda"]
         args.extend(["render", "--output"])
         args.extend(shared_config["conda-source-channel-list"])
         args.extend(variant_args)
         return args
 
-    backend = shared_config.get("backend", DEFAULT_BACKEND)
-    if backend not in ["conda", "mamba"]:
-        raise ValueError(
-            f"Unknown backend: {backend}. Only `conda` and `mamba` are supported."
-        )
-
-    args = [backend]
-
     if command == CondaCommand.SEARCH:
         labels = shared_config.get("labels", [])
         args.extend(
@@ -48,12 +44,10 @@ def conda_cmd_base(command: CondaCommand, shared_config: dict) -> List[str]:
         return args
 
     if command == CondaCommand.BUILD:
-        if backend == "mamba":
-            args = ["conda", "mambabuild"]
-        else:
-            args.extend(["build"])
+        args.extend(["build"])
         args.extend(shared_config["conda-source-channel-list"])
         args.extend(variant_args)
+        args.extend(["--package-format", shared_config["package-format"]])
         return args
 
     raise ValueError(f"unknown command supplied. Got {command}")

src/publish_conda_stack/core.py

@@ -19,7 +19,12 @@
 
 from . import __version__
 from .cmdutil import CondaCommand, conda_cmd_base
-from .util import labels_to_upload_string, strip_label
+from .util import (
+    CONDA_PACKAGE_EXTENSIONS,
+    labels_to_upload_string,
+    strip_conda_package_ext,
+    strip_label,
+)
 
 logger = logging.getLogger()
 logging.basicConfig(format="%(levelname)s: %(message)s", level=logging.INFO)
@@ -173,6 +178,9 @@ def parse_specs(args):
             f"Backend must be either `conda` or `mamba` - found {shared_config['backend']}"
         )
 
+    if "package-format" not in shared_config:
+        shared_config["package-format"] = ".conda"
+
     logger.info(
         f"Using `{shared_config['backend']}` backend. Can be set in config file under the 'backend' key."
     )
@@ -201,6 +209,7 @@ def main():
     result = {
         "version": __version__,
         "backend": shared_config["backend"],
+        "package-format": shared_config["package-format"],
         "found": [],
         "built": [],
         "errors": [],
@@ -498,10 +507,10 @@ def get_rendered_version(
     ).decode()
 
     rendered_filenames = [
-        x for x in subprocess_output.split() if x.endswith(".tar.bz2")
+        x for x in subprocess_output.split() if x.endswith(CONDA_PACKAGE_EXTENSIONS)
     ]
     name_version_builds = [
-        CCPkgName(*Path(x).name.replace(".tar.bz2", "").rsplit("-", maxsplit=2))
+        CCPkgName(*strip_conda_package_ext(Path(x).name).rsplit("-", maxsplit=2))
         for x in rendered_filenames
     ]
 
@@ -590,7 +599,7 @@ def upload_package(
     """
     package_paths = []
     for c_pkg_name in c_pkg_names:
-        pkg_file_name = f"{c_pkg_name.package_name}-{c_pkg_name.version}-{c_pkg_name.build_string}.tar.bz2"
+        pkg_file_name = f"{c_pkg_name.package_name}-{c_pkg_name.version}-{c_pkg_name.build_string}{shared_config['package-format']}"
         BUILD_PKG_DIR = conda_bld_config.build_folder
         CONDA_PLATFORM = f"{conda_bld_config.platform}-{conda_bld_config.arch}"
         pkg_file_path = os.path.join(BUILD_PKG_DIR, CONDA_PLATFORM, pkg_file_name)

src/publish_conda_stack/util.py

@@ -2,6 +2,8 @@
 from itertools import chain
 from typing import List, Tuple, Union
 
+CONDA_PACKAGE_EXTENSIONS = (".tar.bz2", ".conda")
+
 
 def labels_to_upload_string(label_list: List[str]) -> str:
     """generates a string suitable for anaconda upload
@@ -53,10 +55,26 @@ def strip_label(channel_string: str) -> Tuple[str, Union[str, None]]:
     >>> strip_label("some-channel")
     ('some-channel', None)
     """
-    regex = re.compile("/label/" + "(?P<label>[a-zA-Z0-9\-]+)" + "\Z")
+    regex = re.compile("/label/" + r"(?P<label>[a-zA-Z0-9\-]+)" + r"\Z")
     res = regex.search(channel_string)
     if res is None:
         return channel_string, None
     else:
         label = res.groupdict()["label"]
         return channel_string.split(f"/label/{label}")[0], label
+
+
+def strip_conda_package_ext(file_name: str) -> str:
+    """Remove the conda package extension from package file name
+
+    >>> strip_conda_package_ext("some-fancy-package-1.8.0-bld.tar.bz2")
+    'some-fancy-package-1.8.0-bld'
+    >>> strip_conda_package_ext("some-fancy-package-1.8.0-bld.conda")
+    'some-fancy-package-1.8.0-bld'
+    >>> strip_conda_package_ext("some-fancy-package-1.8.0-bld.nocondaext")
+    'some-fancy-package-1.8.0-bld.nocondaext'
+    """
+    for ext in CONDA_PACKAGE_EXTENSIONS:
+        if file_name.endswith(ext):
+            return file_name.removesuffix(ext)
+    return file_name

tests/test_cmdutil.py

@@ -8,6 +8,7 @@ def minimal_shared_config():
     return {
         "conda-source-channel-list": ["-c", "test-forge"],
         "upload-channel": "test-upload-forge",
+        "package-format": ".conda",
     }
 
 
@@ -24,38 +25,21 @@ def test_conda_default(command, minimal_shared_config):
     assert cmd_base[0] == "conda"
 
 
-@pytest.mark.parametrize(
-    "backend",
-    [
-        "conda",
-        "mamba",
-    ],
-)
 @pytest.mark.parametrize(
     "command",
     [
         CondaCommand.SEARCH,
         CondaCommand.BUILD,
     ],
 )
-def test_conda_backend_config(command, backend, minimal_shared_config):
-    minimal_shared_config.update({"backend": backend})
+def test_conda_backend_config(command, minimal_shared_config):
+    minimal_shared_config.update({"backend": "conda"})
     cmd_base = conda_cmd_base(command, minimal_shared_config)
-    if command == CondaCommand.BUILD and backend == "mamba":
-        # special case invocation of boa via conda mambabuild
-        assert cmd_base[0:2] == ["conda", "mambabuild"]
-    else:
-        assert cmd_base[0] == backend
 
+    assert cmd_base[0] == "conda"
 
-@pytest.mark.parametrize(
-    "backend",
-    [
-        "conda",
-        "mamba",
-    ],
-)
-def test_conda_backend_render_always_conda(backend, minimal_shared_config):
+
+def test_conda_backend_render_always_conda(minimal_shared_config):
     command = CondaCommand.RENDER
     cmd_base = conda_cmd_base(command, minimal_shared_config)
 
@@ -92,7 +76,10 @@ def test_labels_added_to_search(labels, minimal_shared_config):
                 "test-upload-forge",
             ],
         ),
-        (CondaCommand.BUILD, ["conda", "build", "-c", "test-forge"]),
+        (
+            CondaCommand.BUILD,
+            ["conda", "build", "-c", "test-forge", "--package-format", ".conda"],
+        ),
     ],
 )
 def test_expected_command(command, expected, minimal_shared_config):