calkit-python 0.11.0__tar.gz → 0.11.2__tar.gz

{calkit_python-0.11.0 → calkit_python-0.11.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: calkit-python
-Version: 0.11.0
+Version: 0.11.2
 Summary: Reproducibility simplified.
 Project-URL: Homepage, https://github.com/calkit/calkit
 Project-URL: Issues, https://github.com/calkit/calkit/issues

{calkit_python-0.11.0 → calkit_python-0.11.2}/calkit/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.11.0"
+__version__ = "0.11.2"
 
 from .core import *
 from . import git

{calkit_python-0.11.0 → calkit_python-0.11.2}/calkit/cli/main.py

@@ -93,9 +93,9 @@ def clone(
     if location is not None:
         cmd.append(location)
     try:
-        subprocess.call(cmd)
-    except Exception as e:
-        raise_error(str(e))
+        subprocess.check_call(cmd)
+    except subprocess.CalledProcessError:
+        raise_error("Failed to clone with Git")
     if location is None:
         location = url.split("/")[-1].removesuffix(".git")
     typer.echo(f"Moving into repo dir: {location}")
@@ -109,7 +109,10 @@ def clone(
                 calkit.dvc.set_remote_auth(remote_name=name)
     # DVC pull
     if not no_dvc_pull:
-        subprocess.call(["dvc", "pull"])
+        try:
+            subprocess.check_call(["dvc", "pull"])
+        except subprocess.CalledProcessError:
+            raise_error("Failed to pull from DVC remote(s)")
 
 
 @app.command(name="status")

{calkit_python-0.11.0 → calkit_python-0.11.2}/calkit/cli/new.py

@@ -827,7 +827,7 @@ def new_publication(
     else:
         template_type = None
     # Check all of our inputs
-    if template_type not in ["latex"]:
+    if template_type is not None and template_type not in ["latex"]:
         raise_error(f"Unknown template type '{template_type}'")
     if env_name is not None and template_type != "latex":
         raise_error("Environments can only be created for latex templates")

{calkit_python-0.11.0 → calkit_python-0.11.2}/calkit/cloud.py

@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-import os
+import warnings
 from functools import partial
 from typing import Literal
 
@@ -35,6 +35,7 @@ def get_token() -> str:
         _tokens[get_base_url()] = token
     # TODO: Check for expiration
     if token is None:
+        warnings.warn("No token found; attempting email+password auth")
         return auth()
     return token
 
@@ -50,10 +51,12 @@ def get_headers(headers: dict | None = None) -> dict:
 def auth() -> str:
     """Authenticate with the server and save a token."""
     cfg = config.read()
+    if cfg.email is None or cfg.password is None:
+        raise ValueError("Config is missing email or password")
     base_url = get_base_url()
     resp = requests.post(
         base_url + "/login/access-token",
-        data=dict(username=cfg.username, password=cfg.password),
+        data=dict(username=cfg.email, password=cfg.password),
     )
     token = resp.json()["access_token"]
     _tokens[base_url] = token

{calkit_python-0.11.0 → calkit_python-0.11.2}/calkit/conda.py

@@ -2,14 +2,43 @@
 
 import json
 import os
+import re
 import subprocess
 
+from packaging.specifiers import SpecifierSet
+from packaging.version import Version
 from pydantic import BaseModel
 
 import calkit
 from calkit import ryaml
 
 
+def _check_single(req: str, actual: str, conda: bool = False) -> bool:
+    """Helper function for checking actual versions against requirements."""
+    req_name = re.split("[=<>]", req)[0]
+    req_spec = req.removeprefix(req_name)
+    if conda and req_spec.startswith("="):
+        req_spec = "=" + req_spec
+        if not req_spec.endswith(".*"):
+            req_spec += ".*"
+    actual_name, actual_vers = re.split("[=<>]+", actual, maxsplit=1)
+    if actual_name != req_name:
+        return False
+    actual_spec = actual.removeprefix(actual_name)
+    if conda and actual_spec.startswith("="):
+        actual_spec = "=" + actual_spec
+    version = Version(actual_vers)
+    spec = SpecifierSet(req_spec)
+    return spec.contains(version)
+
+
+def _check_list(req: str, actual: list[str], conda: bool = False) -> bool:
+    for installed in actual:
+        if _check_single(req, installed, conda=conda):
+            return True
+    return False
+
+
 class EnvCheckResult(BaseModel):
     env_exists: bool | None = None
     env_needs_export: bool | None = None
@@ -127,45 +156,23 @@ def check_env(
                 required_conda_deps.append(dep.replace("==", "="))
         log_func("Checking conda dependencies")
         for dep in required_conda_deps:
-            dep_split = dep.split("=")
-            package = dep_split[0]
-            if len(dep_split) > 1:
-                version = dep_split[1]
-            else:
-                version = None
-            if version is not None and dep not in existing_conda_deps:
+            is_okay = _check_list(
+                req=dep, actual=existing_conda_deps, conda=True
+            )
+            if not is_okay:
                 log_func(f"Found missing dependency: {dep}")
                 env_needs_rebuild = True
                 break
-            elif version is None:
-                # TODO: This does not handle specification of only major or
-                # major+minor version
-                if package not in [
-                    d.split("=")[0] for d in existing_conda_deps
-                ]:
-                    log_func(f"Found missing dependency: {dep}")
-                    env_needs_rebuild = True
-                    break
         if not env_needs_rebuild and not relaxed:
             log_func("Checking pip dependencies")
             for dep in required_pip_deps:
-                dep_split = dep.split("==")
-                package = dep_split[0]
-                if len(dep_split) > 1:
-                    version = dep_split[1]
-                else:
-                    version = None
-                if version is not None and dep not in existing_pip_deps:
+                is_okay = _check_list(
+                    req=dep, actual=existing_pip_deps, conda=False
+                )
+                if not is_okay:
                     env_needs_rebuild = True
                     log_func(f"Found missing dependency: {dep}")
                     break
-                elif version is None:
-                    if package not in [
-                        d.split("==")[0] for d in existing_pip_deps
-                    ]:
-                        log_func(f"Found missing dependency: {dep}")
-                        env_needs_rebuild = True
-                        break
     if env_needs_rebuild:
         res.env_needs_rebuild = True
         log_func(f"Rebuilding {env_name} since it does not match spec")

{calkit_python-0.11.0 → calkit_python-0.11.2}/calkit/config.py

@@ -48,6 +48,7 @@ class Settings(BaseSettings):
         env_prefix="CALKIT" + get_env_suffix(sep="_") + "_",
     )
     username: str | None = None
+    email: str | None = None
     token: str | None = None
     dvc_token: str | None = None
     dataframe_engine: Literal["pandas", "polars"] = "pandas"

{calkit_python-0.11.0 → calkit_python-0.11.2}/calkit/core.py

@@ -16,13 +16,14 @@ except ImportError:
     UTC = _timezone.utc
 
 from datetime import datetime
-
 from typing import Literal
 
 import ruamel.yaml
 from git import Repo
 from git.exc import InvalidGitRepositoryError
 
+from calkit.models import ProjectInfo
+
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__package__)
 
@@ -60,7 +61,9 @@ def find_project_dirs(relative=False, max_depth=3) -> list[str]:
 
 
 def load_calkit_info(
-    wdir=None, process_includes: bool | str | list[str] = False
+    wdir=None,
+    process_includes: bool | str | list[str] = False,
+    as_pydantic: bool = False,
 ) -> dict:
     """Load Calkit project information.
 
@@ -99,6 +102,8 @@ def load_calkit_info(
                         with open(include_fpath) as f:
                             include_data = ryaml.load(f)
                         info[kind][obj_name] |= include_data
+    if as_pydantic:
+        return ProjectInfo.model_validate(info)
     return info
 
 

{calkit_python-0.11.0 → calkit_python-0.11.2}/calkit/models.py

@@ -42,6 +42,7 @@ class Publication(_CalkitObject):
         "journal-article",
         "conference-paper",
         "presentation",
+        "proposal",
         "poster",
         "report",
         "blog",
@@ -106,6 +107,7 @@ class ProcedureInput(BaseModel):
     description : str
         Optional longer description of the input.
     """
+
     name: str | None = None
     dtype: Literal["int", "bool", "str", "float"] = None
     units: str | None = None
@@ -143,6 +145,32 @@ class Procedure(BaseModel):
     imported_from: str | None = None
 
 
+class Release(BaseModel):
+    kind: Literal["project", "publication", "dataset", "model", "figure"]
+    url: str | None = None
+    doi: str | None = None
+    has_suffix: bool = False
+
+
+class ProjectRelease(Release):
+    kind: Literal["project"]
+
+
+class PublicationRelease(Release):
+    kind: Literal["publication"]
+    path: str
+
+
+class DatasetRelease(Release):
+    kind: Literal["dataset"]
+    path: str
+
+
+class ModelRelease(Release):
+    kind: Literal["model"]
+    path: str
+
+
 class ProjectInfo(BaseModel):
     """All of the project's information or metadata, written to the
     ``calkit.yaml`` file.
@@ -178,3 +206,7 @@ class ProjectInfo(BaseModel):
     software: list[Software] = []
     notebooks: list[Notebook] = []
     procedures: dict[str, Procedure] = {}
+    releases: dict[
+        str,
+        ProjectRelease | PublicationRelease | DatasetRelease | ModelRelease,
+    ] = {}

{calkit_python-0.11.0 → calkit_python-0.11.2}/calkit/tests/test_conda.py

@@ -5,7 +5,25 @@ import uuid
 
 import pytest
 
-from calkit.conda import check_env
+from calkit.conda import _check_list, _check_single, check_env
+
+
+def test_check_single():
+    assert _check_single("python=3.12", "python=3.12.18", conda=True)
+    assert _check_single("python=3", "python=3.12.18", conda=True)
+    assert _check_single("python=3.12.18", "python=3.12.18", conda=True)
+    assert _check_single("python>=3.12,<3.13", "python==3.12.18", conda=False)
+
+
+def test_check_list():
+    installed = ["python=3.12.1", "numpy=1.0.11"]
+    assert _check_list("python=3", installed, conda=True)
+    assert _check_list("numpy", installed, conda=True)
+    assert not _check_list("pandas", installed, conda=True)
+    installed = ["python==3.12.1", "numpy==1.0.11"]
+    assert _check_list("python>=3", installed, conda=False)
+    assert _check_list("numpy", installed, conda=False)
+    assert not _check_list("pandas", installed, conda=False)
 
 
 def delete_env(name: str):
@@ -124,3 +142,22 @@ def test_check_env(tmp_dir, env_name):
     )
     res = check_env(relaxed=True)
     assert not res.env_needs_rebuild
+    # Make sure we can handle other ways of specifying versions
+    subprocess.check_call(
+        [
+            "calkit",
+            "new",
+            "conda-env",
+            "--overwrite",
+            "-n",
+            env_name,
+            "python=3.12",
+            "--pip",
+            "numpy>=1",
+        ]
+    )
+    res = check_env()
+    assert res.env_needs_rebuild
+    res = check_env()
+    assert not res.env_needs_export
+    assert not res.env_needs_rebuild