Merge pull request #60 from mariusvniekerk/typer

.github/workflows/pythonpackage.yml

@@ -7,7 +7,7 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       max-parallel: 6
       matrix:
@@ -21,24 +21,29 @@ jobs:
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+        cache-dependency-path: |
+          pyproject.toml
+          ci/requirements.txt
 
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip build
+        python -m pip install --upgrade --quiet pip build flake8 pytest
 
     - name: Lint with flake8
       run: |
-        pip install flake8
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
 
-    - name: Test with pytest
+    - name: Install local editable
       run: |
-        pip install pytest
         pip install -e .
-        pytest .
+
+    - name: Test with pytest
+      run: |
+        pytest --showlocals -vrsx .
         
     - name: Attempt to install library
       run: |
@@ -58,7 +63,7 @@ jobs:
 
     - name: Run the installed package
       run: |
-        export PATH="$PATH:${HOME}/.local/bin"
+        $env:Path = "$PATH;${HOME}/.local/bin"
         black --help
       if: matrix.os == 'windows-latest'
 

.pre-commit-config.yaml

@@ -1,18 +1,14 @@
+minimum_pre_commit_version: '2.9.0'
 repos:
-- repo: https://github.com/pre-commit/mirrors-isort
-  rev: v5.10.1
+- repo: https://github.com/Zac-HD/shed
+  rev: 0.10.5
   hooks:
-      - id: isort
-        args: ["--profile", "black", "--filter-files"]
-
-- repo: https://github.com/psf/black
-  rev: 22.6.0
-  hooks:
-  - id: black
-    language_version: python3
+    - id: shed
+      # args: [--refactor, --py39-plus]
+      types_or: [python, markdown, rst]
 
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v0.971
+  rev: v0.982
   hooks:
   - id: mypy
     additional_dependencies: [types-requests, types-PyYAML]

ci/requirements.txt

@@ -0,0 +1,4 @@
+pip
+build
+pytest
+flake8

condax/__init__.py

@@ -5,4 +5,7 @@
 else:
     from importlib.metadata import version
 
-__version__ = version(__package__)
+try:
+    __version__ = version(__package__)
+except Exception:
+    __version__ = "unknown"

condax/cli.py

@@ -1,49 +1,100 @@
 import sys
+from typing import List, Optional
 
-import click
+import typer
 
 from . import config, core, paths
 
+cli = typer.Typer(
+    name="condax",
+    help="Install and execute applications packaged by conda.",
+    no_args_is_help=True,
+)
 
-@click.group(help="Install and execute applications packaged by conda.")
-def cli():
-    pass
+_OPTION_MAMBA = typer.Option(
+    False,
+    "--mamba",
+    help="Force using mamba.",
+)
+_OPTION_LINK_ACTION = typer.Option(
+    core.LinkConflictAction.ERROR,
+    "--link-conflict",
+    "-l",
+    help=f"""\
+            How to handle conflicts when a link with the same name already exists in
+            `{config.CONFIG.link_destination}`.  If `error` is specified, condax will exit with
+            an error if the link already exists.  If `overwrite` is specified, condax will
+            overwrite the existing link.  If `skip` is specified, condax will skip linking the
+            conflicting executable.""",
+)
 
 
 @cli.command(
-    help=f"""
-    Install a package with condax.
+    help=f"""\
+        Install a package with condax.
 
-    This will install a package into a new conda environment and link the executable
-    provided by it to `{config.CONDAX_LINK_DESTINATION}`.
-    """
-)
-@click.option(
-    "--channel",
-    "-c",
-    multiple=True,
-    help=f"""Use the channels specified to install.  If not specified condax will
-    default to using {config.DEFAULT_CHANNELS}.""",
+        This will install a package into a new conda environment and link the executable
+        provided by it to `{config.CONFIG.link_destination}`.
+        """,
 )
-@click.option(
-    "--link-conflict",
-    "-l",
-    default="error",
-    type=click.Choice([action.value for action in core.LinkConflictAction]),
-    help=f"""How to handle conflicts when a link with the same name already exists in
-    `{config.CONDAX_LINK_DESTINATION}`.  If `error` is specified, condax will exit with
-    an error if the link already exists.  If `overwrite` is specified, condax will
-    overwrite the existing link.  If `skip` is specified, condax will skip linking the
-    conflicting executable.""",
-)
-@click.argument("package")
-def install(channel, package, link_conflict):
+def install(
+    channel: Optional[List[str]] = typer.Option(
+        None,
+        "--channel",
+        "-c",
+        help=f"""\
+            Use the channels specified to install.  If not specified condax will
+            default to using {config.CONFIG.channels}.""",
+    ),
+    link_conflict: core.LinkConflictAction = _OPTION_LINK_ACTION,
+    mamba: bool = _OPTION_MAMBA,
+    package: str = typer.Argument(...),
+):
     if channel is None or (len(channel) == 0):
-        channel = config.DEFAULT_CHANNELS
+        channel = config.CONFIG.channels
+    config.CONFIG.ensure_conda_executable(require_mamba=mamba)
+
     core.install_package(
         package,
         channels=channel,
-        link_conflict_action=core.LinkConflictAction(link_conflict),
+        link_conflict_action=link_conflict,
+    )
+
+
+@cli.command(
+    help=f"""\
+        Inject a package into a condax managed environment.
+
+        This will install a package into an existing condax environment.
+        """,
+)
+def inject(
+    channel: Optional[List[str]] = typer.Option(
+        None,
+        "--channel",
+        "-c",
+        help=f"""\
+            Use the channels specified to install.  If not specified condax will
+            default to using {config.CONFIG.channels}.""",
+    ),
+    mamba: bool = _OPTION_MAMBA,
+    link_conflict: core.LinkConflictAction = _OPTION_LINK_ACTION,
+    include_apps: bool = typer.Option(
+        False, "--include-apps", "Adds applications of injected package to PATH."
+    ),
+    package: str = typer.Argument(..., help="The condax environment inject into."),
+    extra_packages: List[str] = typer.Argument(..., help="Extra packages to install."),
+):
+    if channel is None or (len(channel) == 0):
+        channel = config.CONFIG.channels
+    config.CONFIG.ensure_conda_executable(require_mamba=mamba)
+
+    core.inject_packages(
+        package,
+        extra_packages,
+        channels=channel,
+        link_conflict_action=link_conflict,
+        include_apps=include_apps,
     )
 
 
@@ -55,8 +106,12 @@ def install(channel, package, link_conflict):
     conda environment.
     """
 )
-@click.argument("package")
-def remove(package):
+def remove(
+    package: str,
+    mamba: bool = _OPTION_MAMBA,
+):
+    config.CONFIG.ensure_conda_executable(require_mamba=mamba)
+
     core.remove_package(package)
 
 
@@ -66,8 +121,13 @@ def remove(package):
 
     This can update shell configuration files like `~/.bashrc`."""
 )
-def ensure_path():
-    paths.add_path_to_environment(config.CONDAX_LINK_DESTINATION)
+def ensure_path() -> None:
+    paths.add_path_to_environment(config.CONFIG.link_destination)
+
+
+@cli.command(help="""Display the conda prefix for a condax package.""")
+def prefix(package: str) -> None:
+    typer.echo(core.prefix(package))
 
 
 @cli.command(
@@ -77,29 +137,25 @@ def ensure_path():
     This will update the underlying conda environments(s) to the latest release of a package.
 """
 )
-@click.option(
-    "--all", is_flag=True, help="Set to update all packages installed by condax"
-)
-@click.option(
-    "--link-conflict",
-    "-l",
-    default="error",
-    type=click.Choice([action.value for action in core.LinkConflictAction]),
-    help=f"""How to handle conflicts when a link with the same name already exists in
-    `{config.CONDAX_LINK_DESTINATION}`.  If `error` is specified, condax will exit with
-    an error if the link already exists.  If `overwrite` is specified, condax will
-    overwrite the existing link.  If `skip` is specified, condax will skip linking the
-    conflicting executable.""",
-)
-@click.argument("package", default="", required=False)
-@click.pass_context
-def update(ctx, all, link_conflict, package):
+def update(
+    all: bool = typer.Option(
+        False, "--all", help="Set to update all packages installed by condax"
+    ),
+    link_conflict: core.LinkConflictAction = _OPTION_LINK_ACTION,
+    mamba: bool = _OPTION_MAMBA,
+    package: Optional[str] = typer.Argument(None),
+):
+    config.CONFIG.ensure_conda_executable(require_mamba=mamba)
+    if all and package is not None:
+        typer.echo("Cannot specify --all and a package name")
+        sys.exit(1)
     if all:
-        core.update_all_packages(core.LinkConflictAction(link_conflict))
+        core.update_all_packages(link_conflict)
     elif package:
-        core.update_package(package, core.LinkConflictAction(link_conflict))
+        core.update_package(package, link_conflict)
     else:
-        print(ctx.get_help(), file=sys.stderr)
+        typer.echo("Must specify --all or a package name")
+        sys.exit(1)
 
 
 if __name__ == "__main__":