calkit-python 0.41.19__tar.gz → 0.41.21__tar.gz

calkit_python-0.41.21/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "examples/basic"]
+	path = examples/basic
+	url = https://github.com/calkit/example-basic.git

{calkit_python-0.41.19 → calkit_python-0.41.21}/CONTRIBUTING.md

@@ -98,7 +98,7 @@ This guide will help you get started.
 ## 🎉 Join the community
 
 - Participate in **[GitHub Discussions](https://github.com/calkit/discussions)**.
-- Join our [**Discord**](https://discord.gg/ubb7gAXc) for real-time collaboration.
+- Join our [**Discord**](https://discord.gg/m2MBC79HzD) for real-time collaboration.
 - Follow our updates on [**LinkedIn**](https://linkedin.com/company/calkit).
 
 We appreciate your help in making Calkit better! 🚀

{calkit_python-0.41.19 → calkit_python-0.41.21}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: calkit-python
-Version: 0.41.19
+Version: 0.41.21
 Summary: Reproducibility simplified.
 Project-URL: Homepage, https://calkit.org
 Project-URL: Issues, https://github.com/calkit/calkit/issues
@@ -26,7 +26,7 @@ Requires-Dist: arithmeval
 Requires-Dist: bibtexparser
 Requires-Dist: checksumdir
 Requires-Dist: docx2pdf
-Requires-Dist: dvc==3.67.1
+Requires-Dist: dvc[all]==3.67.1
 Requires-Dist: fastapi
 Requires-Dist: fsspec>=2026.4.0
 Requires-Dist: gitpython
@@ -78,15 +78,16 @@ Description-Content-Type: text/markdown
 
 <!-- INCLUDE: docs/index.md -->
 
-It's six months since you submitted your paper,
-do you know exactly how your figures and results were generated?
-
-You will if they're part of a Calkit project.
+Typical research workflows are horizontally-siloed, i.e.,
+various stages--data collection, analysis, writing--are performed in
+disconnected systems,
+turning research into a slow, error-prone, and tedious
+[waterfall](https://en.wikipedia.org/wiki/Waterfall_model) process.
 
 Calkit helps you integrate code, data, figures, results, publications,
 and more into a cohesive, traceable, and portable _knowledge creation system_,
-so every output can be traced back to its source and reproduced with a
-single command.
+so every output can be traced back to its source (provenance)
+and reproduced with a single command.
 
 With industry standard tools combined into a unified and simplified experience
 tailored for research,

{calkit_python-0.41.19 → calkit_python-0.41.21}/README.md

@@ -19,15 +19,16 @@
 
 <!-- INCLUDE: docs/index.md -->
 
-It's six months since you submitted your paper,
-do you know exactly how your figures and results were generated?
-
-You will if they're part of a Calkit project.
+Typical research workflows are horizontally-siloed, i.e.,
+various stages--data collection, analysis, writing--are performed in
+disconnected systems,
+turning research into a slow, error-prone, and tedious
+[waterfall](https://en.wikipedia.org/wiki/Waterfall_model) process.
 
 Calkit helps you integrate code, data, figures, results, publications,
 and more into a cohesive, traceable, and portable _knowledge creation system_,
-so every output can be traced back to its source and reproduced with a
-single command.
+so every output can be traced back to its source (provenance)
+and reproduced with a single command.
 
 With industry standard tools combined into a unified and simplified experience
 tailored for research,

{calkit_python-0.41.19 → calkit_python-0.41.21}/calkit/cli/list.py

@@ -174,6 +174,40 @@ def list_presentations(
     _list_artifacts("presentations", json_output, declared_only)
 
 
+def _echo_question(n: int, question: str | dict) -> None:
+    """Print a single question in the human-readable YAML-ish listing format.
+
+    String questions are shown as a numbered line. Rich (dict) questions are
+    shown with their text on the first line followed by hypothesis, answer,
+    evidence, and any other fields in YAML-like indented form.
+    """
+    if isinstance(question, str):
+        typer.echo(f"{n}. {question}")
+        return
+    # Copy so popping 'question' doesn't mutate the caller's dict.
+    question = dict(question)
+    text = question.pop("question", "")
+    typer.echo(f"{n}. question: {text}")
+    for k, v in question.items():
+        if isinstance(v, dict):
+            typer.echo(f"    {k}:")
+            for k1, v1 in v.items():
+                typer.echo(f"      {k1}: {v1}")
+        elif isinstance(v, list):
+            typer.echo(f"    {k}:")
+            for item in v:
+                if isinstance(item, dict):
+                    for n1, (k1, v1) in enumerate(item.items()):
+                        if n1 == 0:
+                            typer.echo(f"      - {k1}: {v1}")
+                        else:
+                            typer.echo(f"        {k1}: {v1}")
+                else:
+                    typer.echo(f"        - {item}")
+        else:
+            typer.echo(f"    {k}: {v}")
+
+
 @list_app.command(name="questions")
 def list_questions(
     json_output: Annotated[
@@ -186,7 +220,7 @@ def list_questions(
         typer.echo(json.dumps(questions))
         return
     for n, question in enumerate(questions, start=1):
-        typer.echo(f"{n}. {question}")
+        _echo_question(n, question)
 
 
 @list_app.command(name="publications|pubs")

{calkit_python-0.41.19 → calkit_python-0.41.21}/calkit/cli/main/core.py

@@ -179,11 +179,26 @@ def init(
         typer.Option(
             "--force",
             "-f",
-            help="Force reinitializing DVC if already initialized.",
+            help="Re-initialize even if the project is already initialized.",
         ),
     ] = False,
 ):
     """Initialize the current working directory."""
+    import git
+    from git.exc import InvalidGitRepositoryError
+
+    def _project_is_initialized() -> bool:
+        try:
+            git.Repo(".", search_parent_directories=False)
+        except InvalidGitRepositoryError:
+            return False
+        return os.path.isfile(".dvc/config") and os.path.isfile("calkit.yaml")
+
+    if _project_is_initialized() and not force:
+        raise_error(
+            "This project is already initialized. "
+            "Use --force to re-initialize."
+        )
     subprocess.run(["git", "init"])
     result = calkit.dvc.run_dvc_command(
         ["init"] + (["--force"] if force else [])
@@ -197,13 +212,15 @@ def init(
     # Commit the newly created .dvc directory
     repo = calkit.git.get_repo()
     repo.git.add(".dvc")
-    repo.git.commit("-m", "Initialize DVC")
+    if calkit.git.get_staged_files(repo=repo):
+        repo.git.commit("-m", "Initialize DVC")
     # Create an empty calkit.yaml if one doesn't already exist
     if not os.path.isfile("calkit.yaml"):
         with open("calkit.yaml", "w"):
             pass
         repo.git.add("calkit.yaml")
-        repo.git.commit("-m", "Initialize Calkit")
+        if calkit.git.get_staged_files(repo=repo):
+            repo.git.commit("-m", "Initialize Calkit")
     # TODO: Initialize `dvc.yaml`
     # TODO: Add a sane .gitignore file
     # TODO: Add a sane LICENSE file?
@@ -769,6 +786,8 @@ def add(
         elif to == "git":
             subprocess.call(["git", "add"] + paths)
         elif to == "dvc":
+            for path in paths:
+                calkit.git.ensure_dvc_pointer_is_not_ignored(repo, path)
             calkit.dvc.run_dvc_command(["add"] + paths)
         elif to == "dvc-zip":
             for path in paths:
@@ -882,6 +901,7 @@ def add(
                         f"Adding {path} to DVC since it's already tracked "
                         "with DVC"
                     )
+                    calkit.git.ensure_dvc_pointer_is_not_ignored(repo, path)
                     calkit.dvc.run_dvc_command(["add", path])
             elif posix_path in pipeline_output_storage:
                 # Respect storage explicitly set in the pipeline definition
@@ -926,6 +946,7 @@ def add(
                     typer.echo(f"Would add {path} to DVC (per extension)")
                 else:
                     typer.echo(f"Adding {path} to DVC per its extension")
+                    calkit.git.ensure_dvc_pointer_is_not_ignored(repo, path)
                     calkit.dvc.run_dvc_command(["add", path])
             elif calkit.dvc.zip.is_zip_candidate(path):
                 if dry_run:
@@ -946,6 +967,7 @@ def add(
                     typer.echo(
                         f"Adding {path} to DVC since it's greater than 1 MB"
                     )
+                    calkit.git.ensure_dvc_pointer_is_not_ignored(repo, path)
                     calkit.dvc.run_dvc_command(["add", path])
             else:
                 if dry_run:
@@ -3201,6 +3223,14 @@ def call_dvc(
     and DVC is not installed.
     """
     result = calkit.dvc.run_dvc_command(sys.argv[2:])
+    if result != 0 and len(sys.argv) > 2 and sys.argv[2] == "add":
+        typer.secho(
+            "Hint: If DVC failed because a .dvc pointer file is git-ignored, "
+            "use `calkit add --to=dvc <path>` instead so Calkit can "
+            "automatically manage the gitignore exception.",
+            fg=typer.colors.YELLOW,
+            err=True,
+        )
     sys.exit(result)
 
 

{calkit_python-0.41.19 → calkit_python-0.41.21}/calkit/cli/new.py

@@ -3174,7 +3174,7 @@ def new_release(
         detected_kind, artifact = calkit.releases.find_artifact(path, ck_info)
         if detected_kind is None:
             detected_kind = calkit.detect.detect_artifact_kind(
-                pathlib.Path(path).as_posix()
+                pathlib.Path(path).as_posix(),
             )
         if release_kind is None:
             if detected_kind is None:
@@ -3258,16 +3258,12 @@ def new_release(
         # stored as-is (renamed); folders and whole-project releases are
         # zipped.
         project_name = calkit.detect_project_name(prepend_owner=False)
-        if path == ".":
+        if path == "." or os.path.isdir(path):
             stored_filename = f"{project_name}-{name}.zip"
             is_zip = True
-        elif os.path.isdir(path):
-            folder_name = os.path.basename(os.path.normpath(path))
-            stored_filename = f"{project_name}-{folder_name}-{name}.zip"
-            is_zip = True
         elif os.path.isfile(path):
-            stem, ext = os.path.splitext(os.path.basename(path))
-            stored_filename = f"{project_name}-{stem}-{name}{ext}"
+            _, ext = os.path.splitext(os.path.basename(path))
+            stored_filename = f"{project_name}-{name}{ext}"
             is_zip = False
         else:
             raise_error(f"Release path '{path}' does not exist")

{calkit_python-0.41.19 → calkit_python-0.41.21}/calkit/cli/overleaf.py

@@ -437,7 +437,12 @@ def sync(
         raise_error("No Overleaf sync info found")
     overleaf_sync_dirs = list(overleaf_info.keys())
     if paths is not None:
-        paths = [os.path.dirname(p) if os.path.isfile(p) else p for p in paths]
+        paths = [
+            (os.path.dirname(p) if os.path.isfile(p) else p)
+            .strip()
+            .rstrip("/\\")
+            for p in paths
+        ]
         for path in paths:
             if path not in overleaf_sync_dirs:
                 raise_error(f"Path '{path}' is not synced with Overleaf")
@@ -611,7 +616,12 @@ def get_status(
         raise_error("No Overleaf sync info found")
     overleaf_sync_dirs = list(overleaf_info.keys())
     if paths is not None:
-        paths = [os.path.dirname(p) if os.path.isfile(p) else p for p in paths]
+        paths = [
+            (os.path.dirname(p) if os.path.isfile(p) else p)
+            .strip()
+            .rstrip("/\\")
+            for p in paths
+        ]
         for path in paths:
             if path not in overleaf_sync_dirs:
                 raise_error(f"Path '{path}' is not synced with Overleaf")

{calkit_python-0.41.19 → calkit_python-0.41.21}/calkit/detect.py

@@ -13,6 +13,8 @@ import sys
 from pathlib import Path
 from typing import Literal
 
+import pathspec
+
 NotebookLanguage = Literal["python", "julia", "r"]
 
 
@@ -1549,6 +1551,20 @@ def _is_stdlib_module(module_name: str) -> bool:
     return base_module in common_stdlib
 
 
+_PYTHON_IMPORT_TO_DISTRIBUTION = {
+    "sklearn": "scikit-learn",
+    "skimage": "scikit-image",
+    "cv2": "opencv-python",
+    "PIL": "Pillow",
+    "bs4": "beautifulsoup4",
+    "yaml": "PyYAML",
+    "dateutil": "python-dateutil",
+    "dotenv": "python-dotenv",
+    "serial": "pyserial",
+    "git": "GitPython",
+}
+
+
 def detect_python_dependencies(
     script_path: str | None = None,
     code: str | None = None,
@@ -1614,13 +1630,21 @@ def detect_python_dependencies(
                 if not _is_stdlib_module(module_name):
                     # Get the top-level package name
                     top_level = module_name.split(".")[0]
-                    dependencies.add(top_level)
+                    dependencies.add(
+                        _PYTHON_IMPORT_TO_DISTRIBUTION.get(
+                            top_level, top_level
+                        )
+                    )
         elif isinstance(node, ast.ImportFrom):
             if node.module and node.level == 0:
                 module_name = node.module
                 if not _is_stdlib_module(module_name):
                     top_level = module_name.split(".")[0]
-                    dependencies.add(top_level)
+                    dependencies.add(
+                        _PYTHON_IMPORT_TO_DISTRIBUTION.get(
+                            top_level, top_level
+                        )
+                    )
     return sorted(list(dependencies))
 
 
@@ -1927,6 +1951,21 @@ PRESENTATION_NAMES = {
     "talk.pdf",
 }
 
+DETECTION_IGNORE_FPATH = os.path.join(".calkit", "ignore")
+
+
+def load_detection_ignore(wdir: str | None = None) -> pathspec.PathSpec | None:
+    """Load ``.calkit/ignore`` artifact detection exclusions."""
+    import pathspec
+
+    fpath = DETECTION_IGNORE_FPATH
+    if wdir is not None:
+        fpath = os.path.join(wdir, fpath)
+    if not os.path.isfile(fpath):
+        return None
+    with open(fpath, encoding="utf-8") as f:
+        return pathspec.PathSpec.from_lines("gitwildmatch", f)
+
 
 def _ancestor_dir_names(rel_path: str) -> set[str]:
     """Lower-cased names of the ancestor directories of a "/"-separated path."""
@@ -1938,8 +1977,12 @@ def _path_ext(rel_path: str) -> str:
     return ("." + name.rsplit(".", 1)[-1].lower()) if "." in name else ""
 
 
-def is_figure_path(rel_path: str) -> bool:
+def is_figure_path(
+    rel_path: str, *, ignore: pathspec.PathSpec | None = None
+) -> bool:
     """Whether a repo-relative path looks like an auto-detectable figure."""
+    if ignore is not None and ignore.match_file(rel_path):
+        return False
     ancestors = _ancestor_dir_names(rel_path)
     ext = _path_ext(rel_path)
     if ext in FIGURE_EXTENSIONS and ancestors & FIGURE_DIRS:
@@ -1951,37 +1994,49 @@ def is_figure_path(rel_path: str) -> bool:
     return False
 
 
-def is_dataset_path(rel_path: str) -> bool:
+def is_dataset_path(
+    rel_path: str, *, ignore: pathspec.PathSpec | None = None
+) -> bool:
     """Whether a repo-relative path looks like an auto-detectable dataset."""
+    if ignore is not None and ignore.match_file(rel_path):
+        return False
     return (
         _path_ext(rel_path) in DATASET_EXTENSIONS
         and bool(_ancestor_dir_names(rel_path) & DATA_DIRS)
-        and not is_figure_path(rel_path)
+        and not is_figure_path(rel_path, ignore=ignore)
     )
 
 
-def is_result_path(rel_path: str) -> bool:
+def is_result_path(
+    rel_path: str, *, ignore: pathspec.PathSpec | None = None
+) -> bool:
     """Whether a repo-relative path looks like an auto-detectable result.
 
     A result is a data-like file (JSON, CSV, etc.) under a ``results``-style
     directory. Anything already detected as a figure or dataset is excluded.
     """
+    if ignore is not None and ignore.match_file(rel_path):
+        return False
     return (
         _path_ext(rel_path) in RESULT_EXTENSIONS
         and bool(_ancestor_dir_names(rel_path) & RESULT_DIRS)
-        and not is_figure_path(rel_path)
-        and not is_dataset_path(rel_path)
+        and not is_figure_path(rel_path, ignore=ignore)
+        and not is_dataset_path(rel_path, ignore=ignore)
     )
 
 
-def is_presentation_path(rel_path: str) -> bool:
+def is_presentation_path(
+    rel_path: str, *, ignore: pathspec.PathSpec | None = None
+) -> bool:
     """Whether a repo-relative path looks like an auto-detectable presentation.
 
     Either a slide-deck file (PDF/PPTX/KEY) under a ``slides``/``presentations``
     directory, or a file with a presentation-like name (e.g. ``slides.pdf``,
     ``presentation.pdf``) anywhere. Figures are excluded.
     """
-    if is_figure_path(rel_path):
+    if ignore is not None and ignore.match_file(rel_path):
+        return False
+    if is_figure_path(rel_path, ignore=ignore):
         return False
     name = rel_path.rsplit("/", 1)[-1].lower()
     if name in PRESENTATION_NAMES:
@@ -2018,7 +2073,9 @@ PUBLICATION_NAMES = {
 }
 
 
-def is_publication_path(rel_path: str) -> bool:
+def is_publication_path(
+    rel_path: str, *, ignore: pathspec.PathSpec | None = None
+) -> bool:
     """Whether a repo-relative path looks like an auto-detectable publication.
 
     Either a document (PDF/TeX/DOCX) under a ``paper``/``publication``/
@@ -2026,7 +2083,11 @@ def is_publication_path(rel_path: str) -> bool:
     ``manuscript.pdf``, ``main.tex``) anywhere. Figures and presentations are
     excluded.
     """
-    if is_figure_path(rel_path) or is_presentation_path(rel_path):
+    if ignore is not None and ignore.match_file(rel_path):
+        return False
+    if is_figure_path(rel_path, ignore=ignore) or is_presentation_path(
+        rel_path, ignore=ignore
+    ):
         return False
     name = rel_path.rsplit("/", 1)[-1].lower()
     if name in PUBLICATION_NAMES:
@@ -2036,19 +2097,21 @@ def is_publication_path(rel_path: str) -> bool:
     )
 
 
-def detect_artifact_kind(rel_path: str) -> str | None:
+def detect_artifact_kind(
+    rel_path: str, *, ignore: pathspec.PathSpec | None = None
+) -> str | None:
     """Infer an artifact's release kind from its repo-relative path.
 
     Returns one of ``"figure"``, ``"presentation"``, ``"publication"``, or
     ``"dataset"``, or ``None`` if the path doesn't look like any of these.
     """
-    if is_figure_path(rel_path):
+    if is_figure_path(rel_path, ignore=ignore):
         return "figure"
-    if is_presentation_path(rel_path):
+    if is_presentation_path(rel_path, ignore=ignore):
         return "presentation"
-    if is_publication_path(rel_path):
+    if is_publication_path(rel_path, ignore=ignore):
         return "publication"
-    if is_dataset_path(rel_path):
+    if is_dataset_path(rel_path, ignore=ignore):
         return "dataset"
     return None
 
@@ -2090,6 +2153,7 @@ def _collapse_dataset_folders(paths: list[str]) -> list[str]:
 def detect_figures(
     candidate_paths: list[str],
     reserved_paths: list[str] | tuple[str, ...] = (),
+    ignore: pathspec.PathSpec | None = None,
 ) -> list[str]:
     """Auto-detected figure paths among ``candidate_paths``.
 
@@ -2103,7 +2167,7 @@ def detect_figures(
             for p in candidate_paths
             if not _is_hidden_path(p)
             and not _is_under_any_dir(p, reserved)
-            and is_figure_path(p)
+            and is_figure_path(p, ignore=ignore)
         }
     )
 
@@ -2112,6 +2176,7 @@ def detect_datasets(
     candidate_paths: list[str],
     reserved_paths: list[str] | tuple[str, ...] = (),
     figure_paths: list[str] | tuple[str, ...] = (),
+    ignore: pathspec.PathSpec | None = None,
 ) -> list[str]:
     """Auto-detected dataset paths among ``candidate_paths``.
 
@@ -2126,7 +2191,7 @@ def detect_datasets(
         if not _is_hidden_path(p)
         and not _is_under_any_dir(p, reserved)
         and p not in figset
-        and is_dataset_path(p)
+        and is_dataset_path(p, ignore=ignore)
     }
     return _collapse_dataset_folders(sorted(files))
 
@@ -2134,6 +2199,7 @@ def detect_datasets(
 def detect_results(
     candidate_paths: list[str],
     reserved_paths: list[str] | tuple[str, ...] = (),
+    ignore: pathspec.PathSpec | None = None,
 ) -> list[str]:
     """Auto-detected result paths among ``candidate_paths``.
 
@@ -2147,7 +2213,7 @@ def detect_results(
             for p in candidate_paths
             if not _is_hidden_path(p)
             and not _is_under_any_dir(p, reserved)
-            and is_result_path(p)
+            and is_result_path(p, ignore=ignore)
         }
     )
 
@@ -2155,6 +2221,7 @@ def detect_results(
 def detect_presentations(
     candidate_paths: list[str],
     reserved_paths: list[str] | tuple[str, ...] = (),
+    ignore: pathspec.PathSpec | None = None,
 ) -> list[str]:
     """Auto-detected presentation paths among ``candidate_paths``."""
     reserved = list(reserved_paths)
@@ -2164,7 +2231,7 @@ def detect_presentations(
             for p in candidate_paths
             if not _is_hidden_path(p)
             and not _is_under_any_dir(p, reserved)
-            and is_presentation_path(p)
+            and is_presentation_path(p, ignore=ignore)
         }
     )
 
@@ -2254,18 +2321,28 @@ def detect_project_artifacts(
 
     if ck_info is None:
         ck_info = calkit.load_calkit_info(wdir=wdir)
+    ignore = load_detection_ignore(wdir=wdir)
     reserved = _reserved_artifact_paths(wdir=wdir, ck_info=ck_info)
     candidates = list(
         dict.fromkeys(
             [*list_repo_files(wdir=wdir), *list_dvc_tracked_files(wdir=wdir)]
         )
     )
-    figures = detect_figures(candidates, reserved_paths=reserved)
+    figures = detect_figures(
+        candidates, reserved_paths=reserved, ignore=ignore
+    )
     datasets = detect_datasets(
-        candidates, reserved_paths=reserved, figure_paths=figures
+        candidates,
+        reserved_paths=reserved,
+        figure_paths=figures,
+        ignore=ignore,
+    )
+    results = detect_results(
+        candidates, reserved_paths=reserved, ignore=ignore
+    )
+    presentations = detect_presentations(
+        candidates, reserved_paths=reserved, ignore=ignore
     )
-    results = detect_results(candidates, reserved_paths=reserved)
-    presentations = detect_presentations(candidates, reserved_paths=reserved)
     return {
         "figures": figures,
         "datasets": datasets,

{calkit_python-0.41.19 → calkit_python-0.41.21}/calkit/dvc/zip.py

@@ -499,6 +499,23 @@ def _sync_one(
     # pipeline output that hasn't been produced yet on a fresh run)
     if workspace_hash is None and zip_hash is None:
         return None
+    # Workspace doesn't exist with no prior sync record while syncing to-zip —
+    # there's nothing to push into the zip (e.g., the zip was pulled but
+    # never unzipped into the workspace)
+    if (
+        workspace_hash is None
+        and last_sync_record is None
+        and direction == "to-zip"
+    ):
+        return None
+    # Zip doesn't exist with no prior sync record while syncing to-workspace —
+    # there's nothing to pull into the workspace
+    if (
+        zip_hash is None
+        and last_sync_record is None
+        and direction == "to-workspace"
+    ):
+        return None
     # Deletion + change on the other side is a conflict
     if workspace_deleted and zip_changed and direction == "both":
         raise RuntimeError(

{calkit_python-0.41.19 → calkit_python-0.41.21}/calkit/git.py

@@ -337,3 +337,32 @@ def ensure_path_is_not_ignored(
     if target_repo.ignored(target_path) and _depth < 10:
         ensure_path_is_not_ignored(target_repo, target_path, _depth + 1)
     return True
+
+
+def ensure_dvc_pointer_is_not_ignored(repo, path: str) -> None:
+    """Ensure the .dvc pointer for ``path`` will not be Git-ignored.
+
+    A broad pattern in a ``.gitignore`` (e.g. ``*.pdf*``) can also match the
+    ``<path>.dvc`` pointer DVC commits to Git, causing ``dvc add`` to fail with
+    "bad DVC file name ... is git-ignored". This appends a ``!*.dvc`` negation
+    to the ``.gitignore`` in the pointer's own directory (which wins under Git
+    precedence) so pointers stay tracked. Idempotent.
+    """
+    path = path.replace("\\", "/").rstrip("/")
+    pointer = path + ".dvc"
+    if pointer not in repo.ignored(pointer):
+        return
+    pointer_dir = os.path.dirname(pointer)
+    gitignore_path = os.path.join(repo.working_dir, pointer_dir, ".gitignore")
+    exception = "!*.dvc"
+    existing_lines = []
+    if os.path.isfile(gitignore_path):
+        with open(gitignore_path, "r", encoding="utf-8") as f:
+            existing_lines = f.read().splitlines()
+    if exception in existing_lines:
+        return  # Already present
+    os.makedirs(os.path.dirname(gitignore_path), exist_ok=True)
+    with open(gitignore_path, "a", encoding="utf-8") as f:
+        if existing_lines and existing_lines[-1] != "":
+            f.write("\n")
+        f.write(exception + "\n")

{calkit_python-0.41.19 → calkit_python-0.41.21}/calkit/models/core.py

@@ -351,13 +351,23 @@ class ResultsEvidence(BaseModel):
     explanation: str | None = None
 
 
+class PublicationEvidence(BaseModel):
+    """Evidence in the form of a publication."""
+
+    kind: Literal["publication"] = "publication"
+    path: str
+    explanation: str | None = None
+
+
 class Question(BaseModel):
     """A question the project hopes to answer."""
 
     question: str
     hypothesis: str | None = None
     answer: str | None = None
-    evidence: list[FigureEvidence | ResultsEvidence] | None = None
+    evidence: (
+        list[FigureEvidence | ResultsEvidence | PublicationEvidence] | None
+    ) = None
 
 
 class Dependency(BaseModel):