Added --link-conflict flag

With this flag the user can specify what to do when a link already
exists in the ~/.local/bin directory. The default is `error`, which
will cause the install to fail. The other options are `skip` and
`overwrite`.

Author: Abraham Murciano

condax/cli.py

@@ -13,7 +13,7 @@ def cli():
 @cli.command(
     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}`.
     """
@@ -22,20 +22,35 @@ def cli():
     "--channel",
     "-c",
     multiple=True,
-    help=f"""Use the channels specified to install.  If not specified condax will 
+    help=f"""Use the channels specified to install.  If not specified condax will
     default to using {config.DEFAULT_CHANNELS}.""",
 )
+@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):
+def install(channel, package, link_conflict):
     if channel is None or (len(channel) == 0):
         channel = config.DEFAULT_CHANNELS
-    core.install_package(package, channels=channel)
+    core.install_package(
+        package,
+        channels=channel,
+        link_conflict_action=core.LinkConflictAction(link_conflict)
+    )
 
 
 @cli.command(
     help="""
     Remove a package installed by condax.
-    
+
     This will remove a package installed with condax and destroy the underlying
     conda environment.
     """
@@ -58,20 +73,31 @@ def ensure_path():
 @cli.command(
     help="""
     Update package(s) installed by condax.
-    
+
     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, package):
+def update(ctx, all, link_conflict, package):
     if all:
-        core.update_all_packages()
+        core.update_all_packages(core.LinkConflictAction(link_conflict))
     elif package:
-        core.update_package(package)
+        core.update_package(package, core.LinkConflictAction(link_conflict))
     else:
         print(ctx.get_help(), file=sys.stderr)
 

condax/config.py

@@ -18,4 +18,4 @@
 
 CONDA_ENV_PREFIX_PATH = os.path.expanduser(_config["prefix_path"])
 CONDAX_LINK_DESTINATION = os.path.expanduser(_config["link_destination"])
-DEFAULT_CHANNELS = _config["channels"]
+DEFAULT_CHANNELS = _config["channels"]

condax/core.py

@@ -1,3 +1,4 @@
+from enum import Enum
 import os
 import pathlib
 import subprocess
@@ -7,34 +8,78 @@
 from .config import CONDA_ENV_PREFIX_PATH, CONDAX_LINK_DESTINATION, DEFAULT_CHANNELS
 from .paths import mkpath
 
+class LinkConflictAction(Enum):
+    ERROR = "error"
+    OVERWRITE = "overwrite"
+    SKIP = "skip"
 
-def create_link(exe):
+
+def create_link_windows(exe, link_conflict_action):
     executable_name = os.path.basename(exe)
-    if os.name == "nt":
-        # create a batch file to run our application
-        win_path = pathlib.PureWindowsPath(exe)
-        name_only, _ = os.path.splitext(executable_name)
-        with open(f"{CONDAX_LINK_DESTINATION}/{name_only}.bat", "w") as fo:
-            fo.writelines(
-                [
-                    "@echo off\n",
-                    "REM Entrypoint created by condax\n",
-                    f'CALL "{win_path}" %*',
-                ]
+    # create a batch file to run our application
+    win_path = pathlib.PureWindowsPath(exe)
+    name_only, _ = os.path.splitext(executable_name)
+    bat_path = f"{CONDAX_LINK_DESTINATION}/{name_only}.bat"
+    if os.path.exists(bat_path):
+        if link_conflict_action == LinkConflictAction.ERROR:
+            print(
+                f"Error: link already exists for {executable_name}, use --link-conflict to overwrite or skip",
+                file=sys.stderr,
             )
-    else:
-        print(os.listdir(CONDAX_LINK_DESTINATION))
+            sys.exit(1)
+        elif link_conflict_action == LinkConflictAction.SKIP:
+            print(f"Skipping link for {executable_name} because it already exists", file=sys.stderr)
+            return False
+        elif link_conflict_action == LinkConflictAction.OVERWRITE:
+            print(f"Overwriting existing link {bat_path}", file=sys.stderr)
+            os.remove(bat_path)
+    with open(bat_path, "w") as fo:
+        fo.writelines(
+            [
+                "@echo off\n",
+                "REM Entrypoint created by condax\n",
+                f'CALL "{win_path}" %*',
+            ]
+        )
+    return True
+
+
+def create_link_unix(exe, link_conflict_action):
+    executable_name = os.path.basename(exe)
+    dst = f"{CONDAX_LINK_DESTINATION}/{executable_name}"
+    if link_conflict_action == LinkConflictAction.OVERWRITE and os.path.exists(dst):
+        print(f"Overwriting existing link {dst}", file=sys.stderr)
+        os.remove(dst)
+    try:
         os.symlink(exe, f"{CONDAX_LINK_DESTINATION}/{executable_name}")
+        return True
+    except FileExistsError:
+        if link_conflict_action == LinkConflictAction.ERROR:
+            print(
+                f"Error: link already exists for {executable_name}, use --link-conflict to overwrite or skip",
+                file=sys.stderr,
+            )
+            sys.exit(1)
+        elif link_conflict_action == LinkConflictAction.SKIP:
+            print(f"Skipping link for {executable_name} because it already exists", file=sys.stderr)
+            return False
+
 
+def create_link(exe, link_conflict_action):
+    create_link_func = create_link_windows if sys.platform == "nt" else create_link_unix
+    return create_link_func(exe, link_conflict_action)
 
-def create_links(executables_to_link):
+def create_links(executables_to_link, link_conflict_action):
+    print(os.listdir(CONDAX_LINK_DESTINATION))
+    link_succeeded = {}
     for exe in executables_to_link:
-        create_link(exe)
+        link_succeeded[exe] = create_link(exe, link_conflict_action)
     if len(executables_to_link):
         print("Created the following entrypoint links:", file=sys.stderr)
         for exe in executables_to_link:
-            executable_name = os.path.basename(exe)
-            print(f"    {executable_name}", file=sys.stderr)
+            if link_succeeded[exe]:
+                executable_name = os.path.basename(exe)
+                print(f"    {executable_name}", file=sys.stderr)
 
 
 def remove_links(executables_to_unlink):
@@ -50,11 +95,11 @@ def remove_links(executables_to_unlink):
             print(f"    {executable_name}", file=sys.stderr)
 
 
-def install_package(package, channels=DEFAULT_CHANNELS):
+def install_package(package, channels=DEFAULT_CHANNELS, link_conflict_action=LinkConflictAction.ERROR):
     conda.create_conda_environment(package, channels=channels)
     executables_to_link = conda.detemine_executables_from_env(package)
     mkpath(CONDAX_LINK_DESTINATION)
-    create_links(executables_to_link)
+    create_links(executables_to_link, link_conflict_action)
     print(f"`{package}` has been installed by condax", file=sys.stderr)
 
 
@@ -74,13 +119,13 @@ def remove_package(package):
     print(f"`{package}` has been removed from condax", file=sys.stderr)
 
 
-def update_all_packages():
+def update_all_packages(link_conflict_action=LinkConflictAction.ERROR):
     for package in os.listdir(CONDA_ENV_PREFIX_PATH):
         if os.path.isdir(os.path.join(CONDA_ENV_PREFIX_PATH, package)):
-            update_package(package)
+            update_package(package, link_conflict_action)
 
 
-def update_package(package):
+def update_package(package, link_conflict_action=LinkConflictAction.ERROR):
     exit_if_not_installed(package)
     try:
         executables_already_linked = set(conda.detemine_executables_from_env(package))
@@ -93,7 +138,7 @@ def update_package(package):
         to_create = executables_already_linked - executables_linked_in_updated
 
         remove_links(to_delete)
-        create_links(to_create)
+        create_links(to_create, link_conflict_action)
         print(f"{package} update successfully")
 
     except subprocess.CalledProcessError:

news/link-conflict.md

@@ -0,0 +1,5 @@
+### Added:
+
+* `--link-conflict` flag to specify what to do when a link already exists in the
+  ~/.local/bin directory. The default is `error`, which will cause the install to
+  fail. The other options are `skip` and `overwrite`.