fix: update, add and remove shall not uninstall extra dependencies

With this change unrequested extras dependencies will also be kept when running `install` and are only removed when running `sync`!

docs/cli.md

@@ -204,12 +204,14 @@ poetry install -E mysql -E pgsql
 poetry install --all-extras
 ```
 
-Any extras not specified will always be removed.
+Any extras not specified will be kept but not installed:
 
 ```bash
-poetry install --extras "A B"  # C is removed
+poetry install --extras "A B"  # C is kept if already installed
 ```
 
+If you want to remove unspecified extras, use the `sync` command.
+
 By default `poetry` will install your project's package every time you run `install`:
 
 ```bash

src/poetry/puzzle/transaction.py

@@ -78,7 +78,6 @@ def calculate_operations(
         else:
             priorities = defaultdict(int)
         relevant_result_packages: set[NormalizedName] = set()
-        pending_extra_uninstalls: list[Package] = []  # list for deterministic order
         for result_package in self._result_packages:
             is_unsolicited_extra = False
             if self._marker_env:
@@ -103,9 +102,9 @@ def calculate_operations(
                     relevant_result_packages.add(result_package.name)
 
             if installed_package := self._installed_packages.get(result_package.name):
-                # Extras that were not requested are always uninstalled.
+                # Extras that were not requested are not relevant.
                 if is_unsolicited_extra:
-                    pending_extra_uninstalls.append(installed_package)
+                    pass
 
                 # We have to perform an update if the version or another
                 # attribute of the package has changed (source type, url, ref, ...).
@@ -141,14 +140,9 @@ def calculate_operations(
                     op.skip("Not required")
                 operations.append(op)
 
-        uninstalls: set[NormalizedName] = set()
-        for package in pending_extra_uninstalls:
-            if package.name not in (relevant_result_packages | uninstalls):
-                uninstalls.add(package.name)
-                if package.name not in system_site_packages:
-                    operations.append(Uninstall(package))
-
         if with_uninstalls:
+            uninstalls: set[NormalizedName] = set()
+
             result_packages = {package.name for package in self._result_packages}
             for current_package in self._current_packages:
                 if current_package.name not in (result_packages | uninstalls) and (

tests/installation/test_installer.py

@@ -1400,6 +1400,7 @@ def test_run_with_different_dependency_extras(
 @pytest.mark.parametrize("is_locked", [False, True])
 @pytest.mark.parametrize("is_installed", [False, True])
 @pytest.mark.parametrize("with_extras", [False, True])
+@pytest.mark.parametrize("do_update", [False, True])
 @pytest.mark.parametrize("do_sync", [False, True])
 def test_run_installs_extras_with_deps_if_requested(
     installer: Installer,
@@ -1410,6 +1411,7 @@ def test_run_installs_extras_with_deps_if_requested(
     is_locked: bool,
     is_installed: bool,
     with_extras: bool,
+    do_update: bool,
     do_sync: bool,
 ) -> None:
     package.extras = {canonicalize_name("foo"): [get_dependency("C")]}
@@ -1443,6 +1445,7 @@ def test_run_installs_extras_with_deps_if_requested(
 
     if with_extras:
         installer.extras(["foo"])
+    installer.update(do_update)
     installer.requires_synchronization(do_sync)
     result = installer.run()
     assert result == 0
@@ -1459,7 +1462,7 @@ def test_run_installs_extras_with_deps_if_requested(
         expected_installations_count = 0 if is_installed else 2
         # We only want to uninstall extras if we do a "poetry install" without extras,
         # not if we do a "poetry update" or "poetry add".
-        expected_removals_count = 2 if is_installed else 0
+        expected_removals_count = 2 if is_installed and do_sync else 0
 
     assert installer.executor.installations_count == expected_installations_count
     assert installer.executor.removals_count == expected_removals_count

tests/puzzle/test_transaction.py

@@ -433,8 +433,10 @@ def test_calculate_operations_extras(
     if extras:
         ops = [{"job": "install", "package": Package("a", "1"), "skipped": installed}]
     elif installed:
-        # extras are always removed, even if with_uninstalls is False
-        ops = [{"job": "remove", "package": Package("a", "1")}]
+        if with_uninstalls and sync:
+            ops = [{"job": "remove", "package": Package("a", "1")}]
+        else:
+            ops = []
     else:
         ops = [{"job": "install", "package": Package("a", "1"), "skipped": True}]
 
@@ -494,6 +496,7 @@ def test_calculate_operations_extras_no_redundant_uninstall(extra: str) -> None:
 
     check_operations(
         transaction.calculate_operations(
+            synchronize=True,
             extras=set() if not extra else {canonicalize_name(extra)},
         ),
         ops,