Upgrade: add option to upgrade injected packages

docs/changelog.md

@@ -13,6 +13,7 @@ dev
 - pipx now reinstalls its internal shared libraries when the user executes `reinstall-all`.
 - Made sure shell exit codes from every pipx command are correct.  In the past some (like from `pipx upgrade`) were wrong.  The exit code from `pipx runpip` is now the exit code from the `pip` command run.  The exit code from `pipx list` will be 1 if one or more venvs have problems that need to be addressed.
 - pipx now writes a log file for each pipx command executed to `$PIPX_HOME/logs`, typically `~/.local/pipx/logs`.  pipx keeps the most recent 10 logs and deletes others.
+- `pipx upgrade` and `pipx upgrade-all` now have a `--upgrade-injected` option which directs pipx to also upgrade injected packages.
 - `pipx list` now detects, identifies, and suggests a remedy for venvs with old-internal data (internal venv names) that need to be updated.
 - Added a "Troubleshooting" page to the pipx web documentation for common problems pipx users may encounter.
 

src/pipx/commands/upgrade.py

@@ -12,68 +12,47 @@
 from pipx.venv import Venv, VenvContainer
 
 
-def _upgrade_venv(
-    venv_dir: Path,
+def _upgrade_package(
+    venv: Venv,
+    package: str,
     pip_args: List[str],
-    verbose: bool,
-    *,
-    upgrading_all: bool,
+    is_main_package: bool,
     force: bool,
+    upgrading_all: bool,
 ) -> int:
     """Returns 1 if package version changed, 0 if same version"""
-    if not venv_dir.is_dir():
-        raise PipxError(
-            f"Package is not installed. Expected to find {str(venv_dir)}, "
-            "but it does not exist."
-        )
-
-    venv = Venv(venv_dir, verbose=verbose)
-    package = venv.main_package_name
-
-    if not venv.package_metadata:
-        raise PipxError(
-            f"Not upgrading {red(bold(package))}.  It has missing internal pipx metadata.\n"
-            f"    It was likely installed using a pipx version before 0.15.0.0.\n"
-            f"    Please uninstall and install this package to fix."
-        )
-
     package_metadata = venv.package_metadata[package]
 
     if package_metadata.package_or_url is None:
         raise PipxError(f"Internal Error: package {package} has corrupt pipx metadata.")
 
     package_or_url = parse_specifier_for_upgrade(package_metadata.package_or_url)
     old_version = package_metadata.package_version
-    include_apps = package_metadata.include_apps
-    include_dependencies = package_metadata.include_dependencies
-
-    # Upgrade shared libraries (pip, setuptools and wheel)
-    venv.upgrade_packaging_libraries(pip_args)
 
     venv.upgrade_package(
         package,
         package_or_url,
         pip_args,
-        include_dependencies=include_dependencies,
-        include_apps=include_apps,
-        is_main_package=True,
+        include_dependencies=package_metadata.include_dependencies,
+        include_apps=package_metadata.include_apps,
+        is_main_package=is_main_package,
         suffix=package_metadata.suffix,
     )
-    # TODO 20191026: upgrade injected packages also (Issue #79)
 
     package_metadata = venv.package_metadata[package]
 
     display_name = f"{package_metadata.package}{package_metadata.suffix}"
     new_version = package_metadata.package_version
 
-    expose_apps_globally(
-        constants.LOCAL_BIN_DIR,
-        package_metadata.app_paths,
-        force=force,
-        suffix=package_metadata.suffix,
-    )
+    if package_metadata.include_apps:
+        expose_apps_globally(
+            constants.LOCAL_BIN_DIR,
+            package_metadata.app_paths,
+            force=force,
+            suffix=package_metadata.suffix,
+        )
 
-    if include_dependencies:
+    if package_metadata.include_dependencies:
         for _, app_paths in package_metadata.app_paths_of_dependencies.items():
             expose_apps_globally(
                 constants.LOCAL_BIN_DIR,
@@ -87,29 +66,104 @@ def _upgrade_venv(
             pass
         else:
             print(
-                f"{display_name} is already at latest version {old_version} (location: {str(venv_dir)})"
+                f"{display_name} is already at latest version {old_version} "
+                f"(location: {str(venv.root)})"
             )
         return 0
     else:
         print(
-            f"upgraded package {display_name} from {old_version} to {new_version} (location: {str(venv_dir)})"
+            f"upgraded package {display_name} from {old_version} to {new_version} "
+            f"(location: {str(venv.root)})"
         )
         return 1
 
 
+def _upgrade_venv(
+    venv_dir: Path,
+    pip_args: List[str],
+    verbose: bool,
+    *,
+    include_injected: bool,
+    upgrading_all: bool,
+    force: bool,
+) -> int:
+    """Returns number of packages with changed versions."""
+    if not venv_dir.is_dir():
+        raise PipxError(
+            f"Package is not installed. Expected to find {str(venv_dir)}, "
+            "but it does not exist."
+        )
+
+    venv = Venv(venv_dir, verbose=verbose)
+
+    if not venv.package_metadata:
+        raise PipxError(
+            f"Not upgrading {red(bold(venv_dir.name))}.  It has missing internal pipx metadata.\n"
+            f"    It was likely installed using a pipx version before 0.15.0.0.\n"
+            f"    Please uninstall and install this package to fix."
+        )
+
+    # Upgrade shared libraries (pip, setuptools and wheel)
+    venv.upgrade_packaging_libraries(pip_args)
+
+    versions_updated = 0
+
+    package = venv.main_package_name
+    versions_updated += _upgrade_package(
+        venv,
+        package,
+        pip_args,
+        is_main_package=True,
+        force=force,
+        upgrading_all=upgrading_all,
+    )
+
+    if include_injected:
+        for package in venv.package_metadata:
+            if package == venv.main_package_name:
+                continue
+            versions_updated += _upgrade_package(
+                venv,
+                package,
+                pip_args,
+                is_main_package=False,
+                force=force,
+                upgrading_all=upgrading_all,
+            )
+
+    return versions_updated
+
+
 def upgrade(
-    venv_dir: Path, pip_args: List[str], verbose: bool, *, force: bool
+    venv_dir: Path,
+    pip_args: List[str],
+    verbose: bool,
+    *,
+    include_injected: bool,
+    force: bool,
 ) -> ExitCode:
     """Returns pipx exit code."""
 
-    _ = _upgrade_venv(venv_dir, pip_args, verbose, upgrading_all=False, force=force)
+    _ = _upgrade_venv(
+        venv_dir,
+        pip_args,
+        verbose,
+        include_injected=include_injected,
+        upgrading_all=False,
+        force=force,
+    )
 
-    # Any error in upgrade will raise PipxError from vevn._run_pip()
+    # Any error in upgrade will raise PipxError (e.g. from venv._run_pip())
     return EXIT_CODE_OK
 
 
 def upgrade_all(
-    venv_container: VenvContainer, verbose: bool, *, skip: Sequence[str], force: bool
+    venv_container: VenvContainer,
+    verbose: bool,
+    *,
+    include_injected: bool,
+    skip: Sequence[str],
+    force: bool,
 ) -> ExitCode:
     """Returns pipx exit code."""
     venv_error = False
@@ -126,6 +180,7 @@ def upgrade_all(
                 venv_dir,
                 venv.pipx_metadata.main_package.pip_args,
                 verbose,
+                include_injected=include_injected,
                 upgrading_all=True,
                 force=force,
             )

src/pipx/main.py

@@ -222,10 +222,20 @@ def run_pipx_command(args: argparse.Namespace) -> ExitCode:  # noqa: C901
             force=args.force,
         )
     elif args.command == "upgrade":
-        return commands.upgrade(venv_dir, pip_args, verbose, force=args.force)
+        return commands.upgrade(
+            venv_dir,
+            pip_args,
+            verbose,
+            include_injected=args.include_injected,
+            force=args.force,
+        )
     elif args.command == "upgrade-all":
         return commands.upgrade_all(
-            venv_container, verbose, skip=skip_list, force=args.force
+            venv_container,
+            verbose,
+            include_injected=args.include_injected,
+            skip=skip_list,
+            force=args.force,
         )
     elif args.command == "list":
         return commands.list_packages(venv_container, args.include_injected)
@@ -363,6 +373,11 @@ def _add_upgrade(subparsers, venv_completer) -> None:
         description="Upgrade a package in a pipx-managed Virtual Environment by running 'pip install --upgrade PACKAGE'",
     )
     p.add_argument("package").completer = venv_completer
+    p.add_argument(
+        "--include-injected",
+        action="store_true",
+        help="Also upgrade packages injected into the main app's environment",
+    )
     p.add_argument(
         "--force",
         "-f",
@@ -379,7 +394,11 @@ def _add_upgrade_all(subparsers) -> None:
         help="Upgrade all packages. Runs `pip install -U <pkgname>` for each package.",
         description="Upgrades all packages within their virtual environments by running 'pip install --upgrade PACKAGE'",
     )
-
+    p.add_argument(
+        "--include-injected",
+        action="store_true",
+        help="Also upgrade packages injected into the main app's environment",
+    )
     p.add_argument("--skip", nargs="+", default=[], help="skip these packages")
     p.add_argument(
         "--force",

tests/test_upgrade.py

@@ -55,3 +55,23 @@ def test_upgrade_specifier(pipx_temp_env, capsys):
     assert not run_pipx_cli(["upgrade", f"{name}"])
     captured = capsys.readouterr()
     assert f"upgraded package {name} from {initial_version} to" in captured.out
+
+
+def test_upgrade_include_injected(pipx_temp_env, capsys):
+    assert not run_pipx_cli(["install", "pylint==2.5.3"])
+    assert not run_pipx_cli(["inject", "pylint", "black==18.9.b0"])
+    captured = capsys.readouterr()
+    assert not run_pipx_cli(["upgrade", "--include-injected", "pylint"])
+    captured = capsys.readouterr()
+    assert "upgraded package pylint" in captured.out
+    assert "upgraded package black" in captured.out
+
+
+def test_upgrade_no_include_injected(pipx_temp_env, capsys):
+    assert not run_pipx_cli(["install", "pylint==2.5.3"])
+    assert not run_pipx_cli(["inject", "pylint", "black==18.9.b0"])
+    captured = capsys.readouterr()
+    assert not run_pipx_cli(["upgrade", "pylint"])
+    captured = capsys.readouterr()
+    assert "upgraded package pylint" in captured.out
+    assert "upgraded package black" not in captured.out