calkit-python 0.26.9__tar.gz → 0.26.11__tar.gz

calkit_python-0.26.11/CITATION.cff

@@ -0,0 +1,42 @@
+cff-version: 1.2.0
+message: If you use these files, please cite is using these metadata.
+title: Calkit
+abstract: A project framework and toolkit for single button reproducible
+  research.
+repository-code: https://github.com/calkit/calkit
+authors:
+  - family-names: Bachant
+    given-names: Pete
+    orcid: "0000-0003-4039-6954"
+  - family-names: McCabe
+    given-names: Rebecca
+    orcid:
+  - family-names: Bisht
+    given-names: Mukul
+    orcid:
+identifiers:
+  - description: "All Calkit releases"
+    type: doi
+    value: 10.5281/zenodo.16710624
+  - description: "Calkit v0.26.10"
+    type: doi
+    value: 10.5281/zenodo.16710625
+  - type: swh
+    value: swh:1:dir:50caaf3793cccc64fd9ece2fed488a0110756aff;origin=https://doi.org/10.5281/zenodo.16710624;visit=swh:1:snp:1103646b0c17db58d2485bf2134578b71aec02db;anchor=swh:1:rel:0822fe71a56c06e4097ec9eb128808aeb773e7c2;path=calkit-calkit-c418e8e
+license: MIT
+keywords:
+  - reproducible research
+  - reproducibility
+  - open science
+  - project framework
+  - data science
+  - Python
+  - containerization
+references:
+  - authors:
+      - name: The DVC team and contributors
+        website: https://github.com/iterative
+    doi: 10.5281/zenodo.15828598
+    repository-code: https://github.com/iterative/dvc
+    title: "DVC: Data Version Control - Git for Data & Models"
+    type: software

{calkit_python-0.26.9 → calkit_python-0.26.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: calkit-python
-Version: 0.26.9
+Version: 0.26.11
 Summary: Reproducibility simplified.
 Project-URL: Homepage, https://calkit.org
 Project-URL: Issues, https://github.com/calkit/calkit/issues

{calkit_python-0.26.9 → calkit_python-0.26.11}/calkit/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.26.9"
+__version__ = "0.26.11"
 
 from .core import *  # noqa: F403, I001
 from . import git  # noqa: F401

{calkit_python-0.26.9 → calkit_python-0.26.11}/calkit/cli/check.py

@@ -555,23 +555,18 @@ def check_env_vars(
     dotenv.load_dotenv(dotenv_path=".env")
     ck_info = calkit.load_calkit_info()
     deps = ck_info.get("dependencies", [])
-    env_var_deps = {}
-    for d in deps:
-        if isinstance(d, dict):
-            keys = list(d.keys())
-            if len(keys) > 1:
-                raise_error(
-                    f"Malformed dependency: {d}\n"
-                    "Dependencies with attributes should have a single key "
-                    "(their name)"
-                )
-            name = keys[0]
-            attrs = list(d.values())[0]
-            if attrs.get("kind") == "env-var":
-                env_var_deps[name] = attrs
-    for name, attrs in env_var_deps.items():
+    env_var_dep_names = calkit.get_env_var_dep_names(ck_info)
+    for name in env_var_dep_names:
         if verbose:
             typer.echo(f"Checking for environmental variable '{name}'")
+        attrs = {}
+        for dep in deps:
+            if isinstance(dep, dict) and "name" in dep:
+                attrs = dep
+                break
+            elif isinstance(dep, dict) and list(dep.keys()) == [name]:
+                attrs = dep[name]
+                break
         if name not in os.environ:
             typer.echo(f"Missing env var '{name}'")
             if "default" in attrs:

{calkit_python-0.26.9 → calkit_python-0.26.11}/calkit/cli/main.py

@@ -526,6 +526,20 @@ def save(
             "--no-push", help="Do not push to Git and DVC after committing."
         ),
     ] = False,
+    git_push_args: Annotated[
+        list[str],
+        typer.Option(
+            "--git-push",
+            help="Additional Git args to pass when pushing.",
+        ),
+    ] = [],
+    dvc_push_args: Annotated[
+        list[str],
+        typer.Option(
+            "--dvc-push",
+            help="Additional DVC args to pass when pushing.",
+        ),
+    ] = [],
     verbose: Annotated[
         bool, typer.Option("--verbose", "-v", help="Print verbose output.")
     ] = False,
@@ -579,17 +593,27 @@ def save(
     if not no_push:
         if verbose and not any_dvc:
             typer.echo("Not pushing to DVC since no DVC files were staged")
-        push(no_dvc=not any_dvc)
+        push(
+            no_dvc=not any_dvc, git_args=git_push_args, dvc_args=dvc_push_args
+        )
 
 
 @app.command(name="pull")
 def pull(
     no_check_auth: Annotated[bool, typer.Option("--no-check-auth")] = False,
+    git_args: Annotated[
+        list[str],
+        typer.Option("--git-arg", help="Additional Git args."),
+    ] = [],
+    dvc_args: Annotated[
+        list[str],
+        typer.Option("--dvc-arg", help="Additional DVC args."),
+    ] = [],
 ):
     """Pull with both Git and DVC."""
     typer.echo("Git pulling")
     try:
-        subprocess.check_call(["git", "pull"])
+        subprocess.check_call(["git", "pull"] + git_args)
     except subprocess.CalledProcessError:
         raise_error("Git pull failed")
     typer.echo("DVC pulling")
@@ -601,7 +625,7 @@ def pull(
                 typer.echo(f"Checking authentication for DVC remote: {name}")
                 calkit.dvc.set_remote_auth(remote_name=name)
     try:
-        subprocess.check_call([sys.executable, "-m", "dvc", "pull"])
+        subprocess.check_call([sys.executable, "-m", "dvc", "pull"] + dvc_args)
     except subprocess.CalledProcessError:
         raise_error("DVC pull failed")
 
@@ -610,11 +634,19 @@ def pull(
 def push(
     no_check_auth: Annotated[bool, typer.Option("--no-check-auth")] = False,
     no_dvc: Annotated[bool, typer.Option("--no-dvc")] = False,
+    git_args: Annotated[
+        list[str],
+        typer.Option("--git-arg", help="Additional Git args."),
+    ] = [],
+    dvc_args: Annotated[
+        list[str],
+        typer.Option("--dvc-arg", help="Additional DVC args."),
+    ] = [],
 ):
     """Push with both Git and DVC."""
     typer.echo("Pushing to Git remote")
     try:
-        subprocess.check_call(["git", "push"])
+        subprocess.check_call(["git", "push"] + git_args)
     except subprocess.CalledProcessError:
         raise_error("Git push failed")
     if not no_dvc:
@@ -629,7 +661,9 @@ def push(
                     )
                     calkit.dvc.set_remote_auth(remote_name=name)
         try:
-            subprocess.check_call([sys.executable, "-m", "dvc", "push"])
+            subprocess.check_call(
+                [sys.executable, "-m", "dvc", "push"] + dvc_args
+            )
         except subprocess.CalledProcessError:
             raise_error("DVC push failed")
 
@@ -925,7 +959,11 @@ def run(
     # Get status of Git repo before running
     repo = git.Repo()
     git_rev = repo.head.commit.hexsha
-    git_branch = repo.active_branch.name
+    try:
+        git_branch = repo.active_branch.name
+    except TypeError:
+        # If no branch is checked out, we are in a detached HEAD state
+        git_branch = None
     git_changed_files_before = calkit.git.get_changed_files(repo=repo)
     git_staged_files_before = calkit.git.get_staged_files(repo=repo)
     git_untracked_files_before = calkit.git.get_untracked_files(repo=repo)
@@ -1205,7 +1243,14 @@ def run_in_env(
         ]
         if platform:
             docker_cmd += ["--platform", platform]
-        env_vars = env.get("env-vars", {})
+        env_vars = env.get("env_vars", {})
+        if "env-vars" in env:
+            warn("The 'env-vars' key is deprecated; use 'env_vars' instead.")
+            env_vars.update(env["env-vars"])
+        # Also add any project-level environmental variable dependencies
+        project_env_vars = calkit.get_env_var_dep_names()
+        if project_env_vars:
+            env_vars.update({k: f"${k}" for k in project_env_vars})
         if env_vars:
             for key, value in env_vars.items():
                 if isinstance(value, str):

{calkit_python-0.26.9 → calkit_python-0.26.11}/calkit/cli/notebooks.py

@@ -66,6 +66,9 @@ def execute_notebook(
             "--no-check", help="Do not check environment before executing."
         ),
     ] = False,
+    verbose: Annotated[
+        bool, typer.Option("--verbose", "-v", help="Print verbose output.")
+    ] = False,
 ):
     """Execute notebook and place a copy in the relevant directory.
 
@@ -96,7 +99,7 @@ def execute_notebook(
         "--output",
         fname,
     ]
-    run_in_env(cmd=cmd, env_name=env_name, no_check=no_check)
+    run_in_env(cmd=cmd, env_name=env_name, no_check=no_check, verbose=verbose)
     for to_fmt in to:
         if to_fmt != "notebook":
             try:
@@ -122,4 +125,6 @@ def execute_notebook(
                 fname_out,
             ]
             typer.echo(f"Exporting {to_fmt}")
-            run_in_env(cmd=cmd, env_name=env_name, no_check=True)
+            run_in_env(
+                cmd=cmd, env_name=env_name, no_check=True, verbose=verbose
+            )

{calkit_python-0.26.9 → calkit_python-0.26.11}/calkit/core.py

@@ -312,9 +312,16 @@ def check_system_deps(
     for dep in deps:
         if isinstance(dep, dict):
             keys = list(dep.keys())
-            if len(keys) != 1:
+            # For backwards compatibility, we allow the name to be a single key
+            # or we allow a `name` key to be present
+            if len(keys) != 1 and "name" not in keys:
+                raise ValueError(f"Malformed dependency: {dep}")
+            if len(keys) == 1:
+                dep_name = keys[0]
+            elif "name" in keys:
+                dep_name = dep["name"]
+            else:
                 raise ValueError(f"Malformed dependency: {dep}")
-            dep_name = keys[0]
             dep_kind = dep[dep_name].get("kind", "app")
         else:
             dep_name = re.split("[=<>]", dep)[0]
@@ -323,6 +330,30 @@ def check_system_deps(
             raise ValueError(f"{dep_kind} '{dep_name}' not found")
 
 
+def get_env_var_dep_names(ck_info: dict | None = None) -> list[str]:
+    """Get a list of all environment variable names used in the project."""
+    if ck_info is None:
+        ck_info = load_calkit_info()
+    env_vars = []
+    for dep in ck_info.get("dependencies", []):
+        if isinstance(dep, dict):
+            keys = list(dep.keys())
+            # For backwards compatibility, we allow the name to be a single key
+            # or we allow a `name` key to be present
+            if len(keys) != 1 and "name" not in keys:
+                raise ValueError(f"Malformed dependency: {dep}")
+            if len(keys) == 1:
+                dep_kind = dep[keys[0]].get("kind", "app")
+                if dep_kind == "env-var":
+                    env_vars.append(keys[0])
+            elif dep.get("kind") == "env-var":
+                if "name" in keys:
+                    env_vars.append(dep["name"])
+                else:
+                    raise ValueError(f"Malformed dependency: {dep}")
+    return env_vars
+
+
 def project_and_path_from_path(path: str) -> tuple:
     """Split a path into project and path, respecting the ``CALKIT_PROJECT``
     environmental variable if set.

{calkit_python-0.26.9 → calkit_python-0.26.11}/calkit/models/core.py

@@ -240,6 +240,13 @@ class ProjectStatus(BaseModel):
     message: str | None = None
 
 
+class Dependency(BaseModel):
+    """A system-level dependency, e.g., and app or environmental variable."""
+
+    kind: Literal["app", "env-var"]
+    name: str
+
+
 class ProjectInfo(BaseModel):
     """All of the project's information or metadata, written to the
     ``calkit.yaml`` file.
@@ -267,7 +274,7 @@ class ProjectInfo(BaseModel):
     git_repo_url: str | None = None
     derived_from: DerivedFromProject | None = None
     questions: list[str] = []
-    dependencies: list = []
+    dependencies: list[str | dict[str, str] | Dependency] = []
     parameters: ParametersType | None = None
     metrics: dict[str, Metric] | None = None
     pipeline: Pipeline | None = None

{calkit_python-0.26.9 → calkit_python-0.26.11}/calkit/tests/cli/test_check.py

@@ -1,8 +1,13 @@
 """Tests for ``calkit.cli.check``."""
 
+import os
 import shutil
 import subprocess
 
+import pytest
+
+import calkit
+
 
 def test_check_venv(tmp_dir):
     with open("reqs.txt", "w") as f:
@@ -43,3 +48,27 @@ def test_check_venv(tmp_dir):
     with open("lock.txt") as f:
         lock_txt_3 = f.read()
     assert "polars==1.0.0" in lock_txt_3
+
+
+def test_check_env_vars(tmp_dir):
+    subprocess.check_call(["calkit", "init"])
+    ck_info = {
+        "dependencies": [
+            {"name": "MY_ENV_VAR", "kind": "env-var"},
+            {"name": "MY_APP", "kind": "app"},
+            "something-else",
+            {"MY_OTHER_ENV_VAR": {"kind": "env-var"}},
+        ]
+    }
+    with open("calkit.yaml", "w") as f:
+        calkit.ryaml.dump(ck_info, f)
+    subprocess.check_call(
+        ["calkit", "check", "env-vars"],
+        env=os.environ.copy()
+        | {"MY_ENV_VAR": "value1", "MY_OTHER_ENV_VAR": "value2"},
+    )
+    with pytest.raises(subprocess.CalledProcessError):
+        subprocess.check_call(
+            ["calkit", "check", "env-vars"],
+            env=os.environ.copy() | {"MY_ENV_VAR": "value1"},
+        )

{calkit_python-0.26.9 → calkit_python-0.26.11}/calkit/tests/cli/test_main.py

@@ -407,8 +407,18 @@ def test_run(tmp_dir):
             "main",
         ]
     )
+    subprocess.check_call(
+        ["calkit", "save", "-am", "Create pipeline", "--no-push"]
+    )
     out = subprocess.check_output(["calkit", "run"], text=True)
     print(out)
+    subprocess.check_call(
+        ["calkit", "save", "-am", "Run pipeline", "--no-push"]
+    )
+    # Make sure we can run on a detached head
+    repo = git.Repo()
+    repo.git.checkout("HEAD^")
+    out = subprocess.check_output(["calkit", "run"], text=True)
 
 
 def test_stage_run_info_from_log_content():

{calkit_python-0.26.9 → calkit_python-0.26.11}/calkit/tests/test_core.py

@@ -63,3 +63,18 @@ def test_load_calkit_info(tmp_dir):
     ck_info = calkit.load_calkit_info(process_includes=True)
     assert ck_info["environments"]["env1"]["image"] == "ubuntu"
     assert ck_info["environments"]["env2"]["image"] == "openfoam"
+
+
+def test_get_env_var_dep_names():
+    ck_info = {
+        "dependencies": [
+            {"name": "MY_ENV_VAR", "kind": "env-var"},
+            {"name": "MY_APP", "kind": "app"},
+            "something-else",
+            {"MY_OTHER_ENV_VAR": {"kind": "env-var"}},
+        ]
+    }
+    assert calkit.get_env_var_dep_names(ck_info) == [
+        "MY_ENV_VAR",
+        "MY_OTHER_ENV_VAR",
+    ]