0.4.19 release notes (#3)

* fix base branch * Initial patches 0.4.19 release * undo commit * precommit fix * add patch files * update for generate release notes * allow select unmerged PR * add option to skip commits that requires separate PR to cherry pick * run pre-commit * Update highlight/0.4.19.md Co-authored-by: Wouter-Michiel Vierdag <w-mv@hotmail.com> * Update highlight/0.4.19.md Co-authored-by: Lorenzo Gaifas <brisvag@gmail.com> * Apply suggestions from code review Co-authored-by: Peter Sobolewski <76622105+psobolewskiPhD@users.noreply.github.com> * docs cherry picking * try github format * fix trailing spaces * add new patches * fix link to webpage * update patches * docs cherry-pick * again rebase * update highlight * add patches * add docs pataches * Add patch files * fix generate release notes script * add patch files * Add #6102 as a feature highlight (#4) * add 6102 as a feature highlight * copy edits Co-authored-by: Melissa Weber Mendonça <melissawm@gmail.com> * fix pr link --------- Co-authored-by: Melissa Weber Mendonça <melissawm@gmail.com> * word wrap in highlight, add one pr to performance sequence * Apply suggestions from code review Co-authored-by: Lorenzo Gaifas <brisvag@gmail.com> * Full rewrite of highlights section This ensures it is now dripping with enthusiasm (much deserved) =P * Add API break note * update script to alow multiple notes * filter out mentioned PR * Add deprecations and api changes notes * fix pre-commit * last changes before merge --------- Co-authored-by: wmv_hpomen <w-mv@hotmail.com> Co-authored-by: Lorenzo Gaifas <brisvag@gmail.com> Co-authored-by: Peter Sobolewski <76622105+psobolewskiPhD@users.noreply.github.com> Co-authored-by: Melissa Weber Mendonça <melissawm@gmail.com> Co-authored-by: Juan Nunez-Iglesias <jni@fastmail.com>
napari · Feb 1, 2024 · 49143c4 · 49143c4
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,19 +1,22 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0  # Use the ref you want to point at
+    rev: v4.5.0  # Use the ref you want to point at
     hooks:
       - id: trailing-whitespace
+        exclude: patch_dir
       - id: check-toml
       - id: end-of-file-fixer
+        exclude: patch_dir
       - id: check-yaml
 -   repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 23.7.0
+    rev: 23.10.1
     hooks:
     - id: black
       pass_filenames: true
       exclude: _vendor|vendored|examples
 -   repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.284
+    rev: v0.1.3
     hooks:
       - id: ruff
         exclude: _vendor|vendored
+        args: [--output-format, github]
diff --git a/additional_notes/0.4.19/api changes.md b/additional_notes/0.4.19/api changes.md
@@ -0,0 +1,14 @@
+
+[#6102](https://github.com/napari/napari/pull/6102) added the ability to set
+linear colormaps from black to a named color by using `colormap="color-name"`
+syntax. It turns out that "orange" is both the name of a
+white-to-orange colormap in VisPy, and one of the color names in the color
+dictionary, therefore implicitly a *black-to-orange* colormap! We decided to use
+the new, color-name behavior in this update. So if you are wondering why your
+`imshow(data, colormap='orange')` calls look different — this is why.
+
+In [#6178](https://github.com/napari/napari/pull/6178), the "action" type of
+events emitted when editing Shapes or Points was changed to be more granular.
+The types are no longer "add", "remove", and "change", but "adding", "added",
+"removing", "removed", "changing", and "changed". This gives listeners more
+control over when to take action in response to an event.
diff --git a/additional_notes/0.4.19/deprecations.md b/additional_notes/0.4.19/deprecations.md
@@ -0,0 +1,21 @@
+[#6542](https://github.com/napari/napari/pull/6542) made a number of
+deprecations to the Labels API to simplify it. Rather than having color-related
+properties strewn all over the layer, color control is moved strictly to the
+layer's `colormap`. Here is the full list of deprecated attributes and their
+replacements:
+
+- num_colors: `layer.num_colors` becomes `len(layer.colormap)`.
+  `layer.num_colors = n` becomes `layer.colormap = label_colormap(n)`.
+- `napari.utils.colormaps.LabelColormap` is deprecated and has been renamed to
+  `napari.utils.colormaps.CyclicLabelColormap`.
+- color: `layer.color` becomes `layer.colormap.color_dict`.
+  `layer.color = color_dict` becomes
+  `layer.colormap = DirectLabelColormap(color_dict)`.
+- _background_label: `layer._background_label` is now at
+  `layer.colormap.background_value`.
+- color_mode: `layer.color_mode` is set by setting the colormap using the
+  corresponding colormap type (`CyclicLabelColormap` or `DirectLabelColormap`;
+  these classes can be imported from `napari.utils.colormaps`.).
+- `seed`: was only used for shifting labels around in [0, 1]. It is
+  superseded by `layer.new_colormap()` which was implemented in
+  [#6460](https://github.com/napari/napari/pull/6460).
diff --git a/additional_notes/0.4.19/highlights.md b/additional_notes/0.4.19/highlights.md
@@ -0,0 +1,109 @@
+This release mostly contains a lot of bug fixes and performance improvements.
+But look out for 0.5.0, coming to a software repository near you — we expect to
+release a lot of new features then!
+
+### BIG improvements to the Labels layer
+
+[#3308](https://github.com/napari/napari/pull/3308) closed *many* long-standing
+bugs in the handling of colors in the Labels layer: the color swatch in the
+Labels controls now always matches the color on the canvas, direct color
+mapping with thousands of colors works fine, and shuffling colors (when two
+touching labels coincidentally had the same color) is now much more likely to
+map them to different colors. 🎨🚀🚀🚀
+
+Unfortunately, the fix turned out to have rather
+terrible consequences for the rendering performance of 3D Labels, and each time
+we fixed one thing something else reappeared in a game of bug fix whack-a-mole
+that any programmer would recognize. A great many
+fixes later (
+[#6411](https://github.com/napari/napari/pull/6411),
+[#6439](https://github.com/napari/napari/pull/6439),
+[#6459](https://github.com/napari/napari/pull/6459),
+[#6460](https://github.com/napari/napari/pull/6460),
+[#6461](https://github.com/napari/napari/pull/6461),
+[#6467](https://github.com/napari/napari/pull/6467),
+[#6479](https://github.com/napari/napari/pull/6479),
+[#6520](https://github.com/napari/napari/pull/6520),
+[#6540](https://github.com/napari/napari/pull/6540),
+[#6571](https://github.com/napari/napari/pull/6571),
+[#6580](https://github.com/napari/napari/pull/6580),
+[#6596](https://github.com/napari/napari/pull/6596),
+[#6602](https://github.com/napari/napari/pull/6602),
+[#6607](https://github.com/napari/napari/pull/6607),
+[#6616](https://github.com/napari/napari/pull/6616),
+[#6618](https://github.com/napari/napari/pull/6618)
+) — thank you for your patience! 😅 — Labels are faster than ever
+*and* color accurate. *But*, to get the best performance, if you can use
+8- or 16-bit integers as your data type, you should do so, and if not, you
+should install *numba*, a just-in-time compiler for numerical code in Python.
+(Ultimately, the data sent to the GPU will be 8- or 16-bit, so if you use a
+larger data type, you will pay some conversion cost.)
+
+These improvements in color handling are accompanied by updates to the Labels
+API. You can now easily set a specific color cycle for Labels data. For
+example, to use the famous [Glasbey look-up table/color
+cycle](https://onlinelibrary.wiley.com/doi/10.1002/col.20327), you can combine
+the [`glasbey`](https://pypi.org/project/glasbey/) Python package with the new
+`CyclicLabelColormap` API:
+
+```python
+import glasbey
+from napari.utils.colormaps import CyclicLabelColormap
+# ...
+labels_layer = viewer.add_labels(
+    segmentation, colormap=CyclicLabelColormap(glasbey.create_palette(256))
+)
+```
+
+See the ["Deprecations" section below](#Deprecations) for more information on
+the new API. ([#6542](https://github.com/napari/napari/pull/6542))
+
+### More on colormaps!
+
+Yes, this is the colors update! 🌈
+
+Making image layers with linear colormaps using custom colors is easier than
+ever! You can just do `viewer.add_image(data, color='turquoise')` to get a
+black-to-turquoise linear colormap for that image. For the full list of colors
+available, see the
+[VisPy color dict](https://github.com/vispy/vispy/blob/269ed1ac4d8126421fd5a7eb06a2996d63f46b17/vispy/color/_color_dict.py#L181)
+([#6102](https://github.com/napari/napari/pull/6102)). You can also pass in an
+RGB hex color prefixed with `#`, as in
+`napari.imshow(data, colormap=`#88ff1a`)`.
+
+(For an amusing side note, though, check out the [API Changes](#api-changes)
+note related to this PR. 😅)
+
+### Some technical stuff
+
+If you were worried about those pesky "public access to `qt_viewer` will be
+removed" warnings, fret not! Its removal has been postponed until at least
+0.6.0! We want to spend more time working with the community to ensure your
+use case is supported before pulling out the rug. 🤝 If you are using the
+`qt_viewer` because we don't have another public API to do what you need,
+please [raise an issue](https://github.com/napari/napari/issues/new) so we can
+make sure your use case is supported before we remove it.
+([#6283](https://github.com/napari/napari/pull/6283))
+
+Finally, although we still use pydantic 1.0 objects internally, napari
+installs correctly with both pydantic v1 and pydantic v2. If you wanted to
+upgrade your napari library or plugin to use Pydantic 2, now you can!
+
+Note though, for 0.4.19, the napari bundled app still ships with Pydantic 1.x.
+However, we will bundle v2 starting with 0.5.0, so if you use Pydantic
+internally, now is a good time to check that you are compatible either v2 or
+both v1 and v2
+([#6358](https://github.com/napari/napari/pull/6358)).
+
+### Onwards!
+
+As always, napari is developed by the community, for the community. We want to
+hear from you and help you get your napari visualization and/or plugin use done
+faster! And if napari is missing something you need, we can help you add it! So
+please remember to ask [questions on
+image.sc](https://forum.image.sc/tag/napari), join our [Zulip chat
+room](https://napari.zulipchat.com/), come to our [community
+meetings](https://napari.org/stable/community/meeting_schedule.html), or [tag
+us on Mastodon](https://fosstodon.org/@napari)!
+
+Read on for the full list of changes that went into this release.
diff --git a/cherry_pick_process.py b/cherry_pick_process.py
@@ -1,3 +1,4 @@
+# PYTHON_ARGCOMPLETE_OK
 """
 This is script to cherry-pick commits base on PR labels
 """
@@ -7,6 +8,7 @@
 import os
 from pathlib import Path
 
+import argcomplete
 from git import GitCommandError, Repo
 from tqdm import tqdm
 
@@ -31,9 +33,7 @@ def main():
     parser.add_argument(
         "--first-commits", help="file with list of first commits to cherry pick"
     )
-    parser.add_argument(
-        "--stop-after", help="Stop after this commit", default=0, type=int
-    )
+    parser.add_argument("--stop-after", help="Stop after this PR", default=0, type=int)
     parser.add_argument(
         "--git-main-branch",
         help="The git main branch",
@@ -43,7 +43,14 @@ def main():
     parser.add_argument(
         "--working-dir", help="path to repository", default=LOCAL_DIR, type=Path
     )
+    parser.add_argument(
+        "--skip-commits",
+        nargs="+",
+        help="list of commits to skip as they are already cherry-picked",
+        type=int,
+    )
 
+    argcomplete.autocomplete(parser)
     args = parser.parse_args()
 
     target_branch = f"v{args.milestone}x"
@@ -62,6 +69,7 @@ def main():
         stop_after=args.stop_after,
         base_branch=args.base_branch,
         main_branch=args.git_main_branch,
+        skip_commits=args.skip_commits,
     )
 
 
@@ -94,6 +102,7 @@ def perform_cherry_pick(
     stop_after: int | None,
     base_branch: str,
     main_branch: str = "main",
+    skip_commits: list[int] = None,
 ):
     """
     Perform cherry-pick process
@@ -115,6 +124,8 @@ def perform_cherry_pick(
     main_branch: str
         the main branch of repository, by default is ``main``
         but could be for example ``master``
+    skip_commits: list[int]
+        list of commits to skip as they are already cherry-picked
 
     Returns
     -------
@@ -140,14 +151,17 @@ def perform_cherry_pick(
         if x.milestone == milestone
     ]
 
-    pr_commits_dict = get_pr_commits_dict(repo, base_branch)
+    pr_commits_dict = get_pr_commits_dict(repo, main_branch)
     consumed_pr = get_consumed_pr(repo, target_branch)
 
+    if skip_commits:
+        consumed_pr.update(skip_commits)
+
     # check for errors, may require to reset cache if happens
     for el in pr_targeted_for_release:
         assert el.closed_at is not None, el
 
-    # order PR by merge date, move "first_commits" on begin
+    # order PR by merge date, move "first_commits" to begin
     # (by default PR are ordered by creation date)
     pr_list_base = sorted(
         pr_targeted_for_release,

diff --git a/docs_cherry_pick.py b/docs_cherry_pick.py
@@ -11,9 +11,10 @@
 from tqdm import tqdm
 
 from release_utils import (
+    PR_NUM_PATTERN,
+    REPO_DIR_NAME,
     get_milestone,
     iter_pull_request,
-    pr_num_pattern,
     setup_cache,
 )
 
@@ -44,7 +45,7 @@ def get_consumed_pr():
     base = repo.merge_base(f"docs_{milestone.title}", f"v{milestone.title}x")
 
     for commit in repo.iter_commits(f"{base[0].binsha.hex()}..docs_{milestone.title}"):
-        if (match := pr_num_pattern.search(commit.message)) is not None:
+        if (match := PR_NUM_PATTERN.search(commit.message)) is not None:
             pr_num = int(match[1])
             res.add(pr_num)
     return res
@@ -67,7 +68,7 @@ def get_consumed_pr():
     patch_dir_path.mkdir()
 
 
-repo = Repo(LOCAL_DIR / "napari_repo")
+repo = Repo(LOCAL_DIR / REPO_DIR_NAME)
 repo.git.checkout(f"docs_{milestone.title}")
 
 

diff --git a/generate_release_notes.py b/generate_release_notes.py
@@ -54,6 +54,13 @@
     help="The file with the corrections",
     default=LOCAL_DIR / "name_corrections.yaml",
 )
+parser.add_argument(
+    "--with-pr",
+    help="Include PR numbers for not merged PRs",
+    type=int,
+    default=None,
+    nargs="+",
+)
 
 args = parser.parse_args()
 
@@ -113,9 +120,8 @@ def add_to_users(users_dkt, new_user):
 }
 
 
-for pull in iter_pull_request(f"milestone:{args.milestone} is:merged"):
-    issue = pull.as_issue()
-    assert pull.merged
+def parse_pull(pull):
+    assert pull.merged or pull.number in args.with_pr
 
     commit = repo.get_commit(pull.merge_commit_sha)
 
@@ -143,6 +149,14 @@ def add_to_users(users_dkt, new_user):
         other_pull_requests[pull.number] = {"summary": summary, "repo": GH_REPO}
 
 
+for pull_ in iter_pull_request(f"milestone:{args.milestone} is:merged"):
+    parse_pull(pull_)
+
+if args.with_pr is not None:
+    for pr_num in args.with_pr:
+        pull = repo.get_pull(pr_num)
+        parse_pull(pull)
+
 for pull in iter_pull_request(
     f"milestone:{args.milestone} is:merged", repo=GH_DOCS_REPO
 ):
@@ -181,6 +195,7 @@ def add_to_users(users_dkt, new_user):
 
 
 user_name_pattern = re.compile(r"@([\w-]+)")  # pattern for GitHub usernames
+pr_number_pattern = re.compile(r"#(\d+)")  # pattern for GitHub PR numbers
 
 old_contributors = set()
 
@@ -214,17 +229,30 @@ def add_to_users(users_dkt, new_user):
 print(
     """
 For more information, examples, and documentation, please visit our website:
-https://github.com/napari/napari
+https://napari.org/stable/
 """,
     file=file_handle,
 )
 
 for section, pull_request_dicts in highlights.items():
     print(f"## {section}\n", file=file_handle)
+    section_path = (
+        LOCAL_DIR / "additional_notes" / args.milestone / f"{section.lower()}.md"
+    )
+    mentioned_pr = set()
+    if section_path.exists():
+        with section_path.open() as f:
+            text = f.read()
+        for pr_number in pr_number_pattern.findall(text):
+            mentioned_pr.add(int(pr_number))
+        print(text, file=file_handle)
+
     for number, pull_request_info in pull_request_dicts.items():
+        if number in mentioned_pr:
+            continue
         repo_str = pull_request_info["repo"]
         print(
-            f'- {pull_request_info["summary"]} ([napari/{repo_str}/#{number}](https://{GH}/{GH_USER}/{repo_str}/pull/{number}))',
+            f'- {pull_request_info["summary"]} ([napari/{repo_str}#{number}](https://{GH}/{GH_USER}/{repo_str}/pull/{number}))',
             file=file_handle,
         )
     print("", file=file_handle)