Rebase and fix issues affecting upgrade path, adding duplicate source…

… entry, and when Pipfile.lock does not exist. Adds tests.

news/6299.bugfix.rst

@@ -0,0 +1,2 @@
+- **Bugfix:** Fixed Regression with the ``pipenv update`` routine to allow for package upgrades without requiring an existing lockfile. This change improves the flexibility of the update process by determining which packages require updating and handling cases where the lockfile is absent or partially defined.
+- **Tests Added:** Comprehensive integration tests for the updated functionality, covering scenarios like updating packages without a lockfile, detecting modified entries, handling VCS changes, and verifying the correct application of extras during installation.

pipenv/project.py

@@ -765,11 +765,6 @@ def lockfile(self, categories=None):
             lock_section = lockfile.get(category)
             if lock_section is None:
                 lockfile[category] = lock_section = {}
-            for key in list(lock_section.keys()):
-                norm_key = pep423_name(key)
-                specifier = lock_section[key]
-                del lock_section[key]
-                lockfile[category][norm_key] = specifier
 
         return lockfile
 
@@ -1013,6 +1008,11 @@ def get_index_by_name(self, index_name):
             if source.get("name") == index_name:
                 return source
 
+    def get_index_by_url(self, index_url):
+        for source in self.pipfile_sources():
+            if source.get("url") == index_url:
+                return source
+
     @property
     def sources(self):
         if self.lockfile_exists and hasattr(self.lockfile_content, "keys"):
@@ -1145,7 +1145,9 @@ def remove_packages_from_pipfile(self, packages):
                 del parsed[category][pkg_name]
         self.write_toml(parsed)
 
-    def generate_package_pipfile_entry(self, package, pip_line, category=None):
+    def generate_package_pipfile_entry(
+        self, package, pip_line, category=None, index_name=None
+    ):
         """Generate a package entry from pip install line
         given the installreq package and the pip line that generated it.
         """
@@ -1203,7 +1205,10 @@ def generate_package_pipfile_entry(self, package, pip_line, category=None):
                     break
         else:
             entry["version"] = specifier
-        if hasattr(package, "index"):
+
+        if index_name:
+            entry["index"] = index_name
+        elif hasattr(package, "index"):
             entry["index"] = package.index
 
         if len(entry) == 1 and "version" in entry:

pipenv/routines/graph.py

@@ -34,7 +34,7 @@ def do_graph(project, bare=False, json=False, json_tree=False, reverse=False):
         sys.exit(1)
 
     # Build command arguments list
-    cmd_args = [python_path, pipdeptree_path, "-l"]
+    cmd_args = [python_path, str(pipdeptree_path), "-l"]
 
     # Add flags as needed - multiple flags now supported
     if json:

pipenv/routines/update.py

@@ -11,8 +11,10 @@
 from pipenv.routines.outdated import do_outdated
 from pipenv.routines.sync import do_sync
 from pipenv.utils import err
+from pipenv.utils.constants import VCS_LIST
 from pipenv.utils.dependencies import (
     expansive_install_req_from_line,
+    get_lockfile_section_using_pipfile_category,
     get_pipfile_category_using_lockfile_section,
 )
 from pipenv.utils.processes import run_command
@@ -59,16 +61,17 @@ def do_update(
 
     if not outdated:
         # Pre-sync packages for pipdeptree resolution to avoid conflicts
-        do_sync(
-            project,
-            dev=dev,
-            categories=categories,
-            python=python,
-            bare=bare,
-            clear=clear,
-            pypi_mirror=pypi_mirror,
-            extra_pip_args=extra_pip_args,
-        )
+        if project.lockfile_exists:
+            do_sync(
+                project,
+                dev=dev,
+                categories=categories,
+                python=python,
+                bare=bare,
+                clear=clear,
+                pypi_mirror=pypi_mirror,
+                extra_pip_args=extra_pip_args,
+            )
         upgrade(
             project,
             pre=pre,
@@ -106,12 +109,11 @@ def get_reverse_dependencies(project) -> Dict[str, Set[Tuple[str, str]]]:
     """Get reverse dependencies using pipdeptree."""
     pipdeptree_path = Path(pipdeptree.__file__).parent
     python_path = project.python()
-    cmd_args = [python_path, pipdeptree_path, "-l", "--reverse", "--json-tree"]
+    cmd_args = [python_path, str(pipdeptree_path), "-l", "--reverse", "--json-tree"]
 
     c = run_command(cmd_args, is_verbose=project.s.is_verbose())
     if c.returncode != 0:
         raise PipenvCmdError(c.err, c.out, c.returncode)
-
     try:
         dep_tree = json.loads(c.stdout.strip())
     except json.JSONDecodeError:
@@ -137,7 +139,12 @@ def process_tree_node(n, parents=None):
 
     # Start processing the tree from the root nodes
     for node in dep_tree:
-        process_tree_node(node)
+        try:
+            process_tree_node(node)
+        except Exception as e:  # noqa: PERF203
+            err.print(
+                f"[red bold]Warning[/red bold]: Unable to analyze dependencies: {str(e)}"
+            )
 
     return reverse_deps
 
@@ -166,13 +173,76 @@ def check_version_conflicts(
             specifier_set = SpecifierSet(req_version)
             if not specifier_set.contains(new_version_obj):
                 conflicts.add(dependent)
-        except Exception:
+        except Exception:  # noqa: PERF203
             # If we can't parse the version requirement, assume it's a conflict
             conflicts.add(dependent)
 
     return conflicts
 
 
+def get_modified_pipfile_entries(project, pipfile_categories):
+    """
+    Detect Pipfile entries that have been modified since the last lock.
+    Returns a dict mapping categories to sets of InstallRequirement objects.
+    """
+    modified = defaultdict(dict)
+    lockfile = project.lockfile()
+
+    for pipfile_category in pipfile_categories:
+        lockfile_category = get_lockfile_section_using_pipfile_category(pipfile_category)
+        pipfile_packages = project.parsed_pipfile.get(pipfile_category, {})
+        locked_packages = lockfile.get(lockfile_category, {})
+
+        for package_name, pipfile_entry in pipfile_packages.items():
+            if package_name not in locked_packages:
+                # New package
+                modified[lockfile_category][package_name] = pipfile_entry
+                continue
+
+            locked_entry = locked_packages[package_name]
+            is_modified = False
+
+            # For string entries, compare directly
+            if isinstance(pipfile_entry, str):
+                if pipfile_entry != locked_entry.get("version", ""):
+                    is_modified = True
+
+            # For dict entries, need to compare relevant fields
+            elif isinstance(pipfile_entry, dict):
+                if "version" in pipfile_entry:
+                    if pipfile_entry["version"] != locked_entry.get("version", ""):
+                        is_modified = True
+
+                # Compare VCS fields
+                for key in VCS_LIST:
+                    if key in pipfile_entry:
+                        if (
+                            key not in locked_entry
+                            or pipfile_entry[key] != locked_entry[key]
+                        ):
+                            is_modified = True
+
+                # Compare ref for VCS packages
+                if "ref" in pipfile_entry:
+                    if (
+                        "ref" not in locked_entry
+                        or pipfile_entry["ref"] != locked_entry["ref"]
+                    ):
+                        is_modified = True
+
+                # Compare extras
+                if "extras" in pipfile_entry:
+                    pipfile_extras = set(pipfile_entry["extras"])
+                    locked_extras = set(locked_entry.get("extras", []))
+                    if pipfile_extras != locked_extras:
+                        is_modified = True
+
+            if is_modified:
+                modified[lockfile_category][package_name] = pipfile_entry
+
+    return modified
+
+
 def upgrade(
     project,
     pre=False,
@@ -206,17 +276,14 @@ def upgrade(
         categories.insert(0, "default")
 
     # Get current dependency graph
-    try:
-        reverse_deps = get_reverse_dependencies(project)
-    except Exception as e:
-        err.print(
-            f"[red bold]Warning[/red bold]: Unable to analyze dependencies: {str(e)}"
-        )
-        reverse_deps = {}
+    reverse_deps = get_reverse_dependencies(project)
 
     index_name = None
     if index_url:
-        index_name = add_index_to_pipfile(project, index_url)
+        if project.get_index_by_url(index_url):
+            index_name = project.get_index_by_url(index_url)["name"]
+        else:
+            index_name = add_index_to_pipfile(project, index_url)
 
     if extra_pip_args:
         os.environ["PIPENV_EXTRA_PIP_ARGS"] = json.dumps(extra_pip_args)
@@ -245,76 +312,71 @@ def upgrade(
         )
         sys.exit(1)
 
-    requested_install_reqs = defaultdict(dict)
+    # Create clean package_args first
+    has_package_args = False
+    if package_args:
+        has_package_args = True
+
     requested_packages = defaultdict(dict)
     for category in categories:
         pipfile_category = get_pipfile_category_using_lockfile_section(category)
 
+        # Get modified entries if no explicit packages specified
+        if not package_args and project.lockfile_exists:
+            modified_entries = get_modified_pipfile_entries(project, [pipfile_category])
+            for name, entry in modified_entries[category].items():
+                requested_packages[pipfile_category][name] = entry
+
+        # Process each package arg
         for package in package_args[:]:
             install_req, _ = expansive_install_req_from_line(package, expand_env=True)
-            if index_name:
-                install_req.index = index_name
 
             name, normalized_name, pipfile_entry = project.generate_package_pipfile_entry(
-                install_req, package, category=pipfile_category
-            )
-            project.add_pipfile_entry_to_pipfile(
-                name, normalized_name, pipfile_entry, category=pipfile_category
+                install_req, package, category=pipfile_category, index_name=index_name
             )
+
+            # Only add to Pipfile if explicitly requested
+            if has_package_args:
+                project.add_pipfile_entry_to_pipfile(
+                    name, normalized_name, pipfile_entry, category=pipfile_category
+                )
+
             requested_packages[pipfile_category][normalized_name] = pipfile_entry
-            requested_install_reqs[pipfile_category][normalized_name] = install_req
 
-            # Consider reverse packages in reverse_deps
+            # Handle reverse dependencies
             if normalized_name in reverse_deps:
-                for dependency, req_version in reverse_deps[normalized_name]:
-                    if req_version == "Any":
-                        package_args.append(dependency)
-                        pipfile_entry = project.get_pipfile_entry(
-                            dependency, category=pipfile_category
-                        )
-                        requested_packages[pipfile_category][dependency] = (
-                            pipfile_entry if pipfile_entry else "*"
-                        )
+                for dependency, _ in reverse_deps[normalized_name]:
+                    pipfile_entry = project.get_pipfile_entry(
+                        dependency, category=pipfile_category
+                    )
+                    if not pipfile_entry:
+                        requested_packages[pipfile_category][dependency] = {
+                            normalized_name: "*"
+                        }
                         continue
+                    requested_packages[pipfile_category][dependency] = pipfile_entry
 
-                    try:  # Otherwise we have a specific version requirement
-                        specifier_set = SpecifierSet(req_version)
-                        package_args.append(f"{dependency}=={specifier_set}")
-                        pipfile_entry = project.get_pipfile_entry(
-                            dependency, category=pipfile_category
-                        )
-                        requested_packages[pipfile_category][dependency] = (
-                            pipfile_entry if pipfile_entry else "*"
-                        )
-
-                    except Exception as e:
-                        err.print(
-                            f"[bold][yellow]Warning:[/yellow][/bold] "
-                            f"Unable to parse version specifier for {dependency}: {str(e)}"
-                        )
-
-        if not package_args:
-            err.print("Nothing to upgrade!")
-            return
-        else:
+        # When packages are not provided we simply perform full resolution
+        upgrade_lock_data = None
+        if requested_packages[pipfile_category]:
             err.print(
                 f"[bold][green]Upgrading[/bold][/green] {', '.join(package_args)} in [{category}] dependencies."
             )
 
-        # Resolve package to generate constraints of new package data
-        upgrade_lock_data = venv_resolve_deps(
-            requested_packages[pipfile_category],
-            which=project._which,
-            project=project,
-            lockfile={},
-            pipfile_category=pipfile_category,
-            pre=pre,
-            allow_global=system,
-            pypi_mirror=pypi_mirror,
-        )
-        if not upgrade_lock_data:
-            err.print("Nothing to upgrade!")
-            return
+            # Resolve package to generate constraints of new package data
+            upgrade_lock_data = venv_resolve_deps(
+                requested_packages[pipfile_category],
+                which=project._which,
+                project=project,
+                lockfile={},
+                pipfile_category=pipfile_category,
+                pre=pre,
+                allow_global=system,
+                pypi_mirror=pypi_mirror,
+            )
+            if not upgrade_lock_data:
+                err.print("Nothing to upgrade!")
+                return
 
         complete_packages = project.parsed_pipfile.get(pipfile_category, {})
 
@@ -329,21 +391,29 @@ def upgrade(
             pypi_mirror=pypi_mirror,
         )
 
-        # Verify no conflicts were introduced during resolution
-        for package_name, package_data in full_lock_resolution.items():
-            if package_name in upgrade_lock_data:
-                version = package_data.get("version", "").replace("==", "")
-                if not version:
-                    # Either vcs or file package
-                    continue
-
-        # Update lockfile with verified resolution data
-        for package_name in upgrade_lock_data:
-            correct_package_lock = full_lock_resolution.get(package_name)
-            if correct_package_lock:
-                if category not in lockfile:
-                    lockfile[category] = {}
-                lockfile[category][package_name] = correct_package_lock
+        if upgrade_lock_data is None:
+            for package_name, package_data in full_lock_resolution.items():
+                lockfile[category][package_name] = package_data
+        else:  # Upgrade a subset of packages
+            # Verify no conflicts were introduced during resolution
+            for package_name, package_data in full_lock_resolution.items():
+                if package_name in upgrade_lock_data:
+                    version = package_data.get("version", "").replace("==", "")
+                    if not version:
+                        # Either vcs or file package
+                        continue
+
+            # Update lockfile with verified resolution data
+            for package_name in upgrade_lock_data:
+                correct_package_lock = full_lock_resolution.get(package_name)
+                if correct_package_lock:
+                    if category not in lockfile:
+                        lockfile[category] = {}
+                    lockfile[category][package_name] = correct_package_lock
+
+        # reset package args in case of multiple categories being processed
+        if has_package_args is False:
+            package_args = []
 
     lockfile.update({"_meta": project.get_lockfile_meta()})
     project.write_lockfile(lockfile)