calkit-python 0.30.9__tar.gz → 0.30.11__tar.gz

{calkit_python-0.30.9 → calkit_python-0.30.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: calkit-python
-Version: 0.30.9
+Version: 0.30.11
 Summary: Reproducibility simplified.
 Project-URL: Homepage, https://calkit.org
 Project-URL: Issues, https://github.com/calkit/calkit/issues

{calkit_python-0.30.9 → calkit_python-0.30.11}/calkit/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.30.9"
+__version__ = "0.30.11"
 
 from .core import *  # noqa: F403, I001
 from . import git  # noqa: F401

{calkit_python-0.30.9 → calkit_python-0.30.11}/calkit/cli/main.py

@@ -82,9 +82,20 @@ app.add_typer(cloud_app, name="cloud", help="Interact with a Calkit Cloud.")
 app.add_typer(slurm_app, name="slurm", help="Work with SLURM.")
 
 # Constants for version control auto-ignore
-AUTO_IGNORE_SUFFIXES = [".DS_Store", ".env", ".pyc", ".synctex.gz"]
+AUTO_IGNORE_SUFFIXES = [
+    ".DS_Store",
+    ".env",
+    ".pyc",
+    ".synctex.gz",
+    ".ipynb_checkpoints",
+]
 AUTO_IGNORE_PATHS = [os.path.join(".dvc", "config.local")]
-AUTO_IGNORE_PREFIXES = [".venv", "__pycache__"]
+AUTO_IGNORE_PREFIXES = [
+    ".venv",
+    "__pycache__",
+    ".ipynb_checkpoints",
+    ".calkit/overleaf/",
+]
 # Constants for version control auto-add to DVC
 DVC_EXTENSIONS = [
     ".png",
@@ -990,6 +1001,9 @@ def run(
     """Check dependencies and run the pipeline."""
     os.environ["CALKIT_PIPELINE_RUNNING"] = "1"
     dotenv.load_dotenv(dotenv_path=".env", verbose=verbose)
+    ck_info = calkit.load_calkit_info()
+    # Set env vars
+    calkit.set_env_vars(ck_info=ck_info)
     if not quiet:
         typer.echo("Getting system information")
     system_info = calkit.get_system_info()
@@ -1013,7 +1027,6 @@ def run(
         os.environ.pop("CALKIT_PIPELINE_RUNNING", None)
         raise_error(str(e))
     # Compile the pipeline
-    ck_info = calkit.load_calkit_info()
     if ck_info.get("pipeline", {}):
         if not quiet:
             typer.echo("Compiling DVC pipeline")
@@ -1251,6 +1264,7 @@ def run_in_env(
 ):
     dotenv.load_dotenv(dotenv_path=".env", verbose=verbose)
     ck_info = calkit.load_calkit_info(process_includes="environments")
+    calkit.set_env_vars(ck_info=ck_info)
     envs = ck_info.get("environments", {})
     if not envs:
         raise_error("No environments defined in calkit.yaml")
@@ -1314,6 +1328,8 @@ def run_in_env(
         if "env-vars" in env:
             warn("The 'env-vars' key is deprecated; use 'env_vars' instead.")
             env_vars.update(env["env-vars"])
+        # Add project-level env vars (non-secret)
+        env_vars.update(ck_info.get("env_vars", {}))
         # Also add any project-level environmental variable dependencies
         project_env_vars = calkit.get_env_var_dep_names()
         if project_env_vars:
@@ -1668,6 +1684,7 @@ def run_procedure(
         return value
 
     ck_info = calkit.load_calkit_info(process_includes="procedures")
+    calkit.set_env_vars(ck_info=ck_info)
     procs = ck_info.get("procedures", {})
     if name not in procs:
         raise_error(f"'{name}' is not defined as a procedure")

{calkit_python-0.30.9 → calkit_python-0.30.11}/calkit/cli/overleaf.py

@@ -159,11 +159,7 @@ def import_publication(
         shutil.rmtree(overleaf_project_dir)
     # Clone the Overleaf project
     typer.echo("Cloning Overleaf project")
-    git.Repo.clone_from(
-        git_clone_url,
-        overleaf_project_dir,
-        depth=1,
-    )
+    git.Repo.clone_from(git_clone_url, overleaf_project_dir)
     # Detect target path if not specified
     if target_path is None:
         ol_contents = os.listdir(overleaf_project_dir)

{calkit_python-0.30.9 → calkit_python-0.30.11}/calkit/core.py

@@ -602,3 +602,23 @@ def get_md5(path: str, exclude_files: list[str] | None = None) -> str:
         with open(path) as f:
             content = f.read()
         return hashlib.md5(content.encode()).hexdigest()
+
+
+def set_env_vars(ck_info: dict, cli: bool = True) -> None:
+    """Set environmental variables according to the values read from
+    ``calkit.yaml``.
+    """
+    env_vars = ck_info.get("env_vars", {})
+    if not isinstance(env_vars, dict):
+        msg = (
+            "Environmental variables in Calkit project info must be a "
+            "map/dictionary"
+        )
+        if cli:
+            from calkit.cli import raise_error
+
+            raise_error(msg)
+        else:
+            raise ValueError(msg)
+    for k, v in env_vars.items():
+        os.environ[str(k)] = str(v)

{calkit_python-0.30.9 → calkit_python-0.30.11}/calkit/tests/cli/test_main.py

@@ -50,6 +50,18 @@ def test_run_in_env(tmp_dir):
         stdin=stdin,
         check=True,
     )
+    # Check that we can pass project env vars into the container
+    ck_info = calkit.load_calkit_info()
+    ck_info["env_vars"] = {"MY_COOL_ENV_VAR": "my cool value"}
+    with open("calkit.yaml", "w") as f:
+        calkit.ryaml.dump(ck_info, f)
+    p = subprocess.run(
+        ["calkit", "xenv", "echo", "$MY_COOL_ENV_VAR"],
+        text=True,
+        capture_output=True,
+        check=True,
+    )
+    assert "my cool value" in p.stdout
     # Now let's create a 2nd Docker env and make sure we need to call it by
     # name when trying to run
     subprocess.check_call(
@@ -452,6 +464,19 @@ def test_run(tmp_dir):
     subprocess.check_call(
         ["calkit", "save", "-am", "Run pipeline", "--no-push"]
     )
+    # Test that we can set env vars at the project level
+    ck_info = calkit.load_calkit_info()
+    ck_info["env_vars"] = {"MY_ENV_VAR": "some-value"}
+    with open("calkit.yaml", "w") as f:
+        calkit.ryaml.dump(ck_info, f)
+    with open("script.py", "w") as f:
+        f.write("import os\nprint(os.environ['MY_ENV_VAR'])")
+    out = subprocess.check_output(["calkit", "run"], text=True)
+    print(out)
+    assert "some-value" in 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^")

{calkit_python-0.30.9 → calkit_python-0.30.11}/docs/dependencies.md

@@ -57,3 +57,14 @@ can be used to define these variables.
 in lieu of directly editing `.env`.
 `calkit check env-vars` can also be run to check for missing variables,
 prompting the user for their values and setting them in `.env`.
+
+Additional (non-secret) environmental variables can be set at the project
+level in `calkit.yaml` in the `env_vars` map:
+
+```yaml
+env_vars:
+  MY_ENV_VAR_NAME: the-value-here
+  ANOTHER_VAR: another value
+```
+
+These will then be set for calls to the `run` and `xenv` commands.