EMCEE Batch Submit CLI Tool

.github/workflows/gempyor-ci.yml

@@ -43,6 +43,7 @@ jobs:
         shell: bash
       - name: Run gempyor tests
         run: |
+          export FLEPI_PATH=$(pwd)
           cd flepimop/gempyor_pkg
           pytest --exitfirst
         shell: bash

.gitignore

@@ -78,3 +78,6 @@ flepimop/gempyor_pkg/.coverage
 
 # Environment variables
 .env
+
+# info/ directory
+info/**/*.json

flepimop/gempyor_pkg/pyproject.toml

@@ -20,11 +20,13 @@ dependencies = [
     "emcee",
     "graphviz",
     "h5py",
+    "Jinja2",
     "matplotlib",
     "numba>=0.53.1",
     "numpy",
     "pandas",
     "pyarrow",
+    "pydantic",
     "scipy",
     "seaborn",
     "sympy",
@@ -51,7 +53,8 @@ gempyor-simulate = "gempyor.simulate:_deprecated_simulate"
 
 [tool.setuptools]
 package-dir = {"" = "src"}
-include-package-data = false
+include-package-data = true
+package-data = { "gempyor" = ["templates/*.j2"] }
 
 [tool.setuptools.packages.find]
 where = ["src"]

flepimop/gempyor_pkg/src/gempyor/_jinja.py

@@ -0,0 +1,120 @@
+"""
+Internal Jinja2 template rendering utilities.
+
+This module contains utilities for finding and rendering Jinja2 templates. This module
+is tightly coupled to the organization of the package and not intended for external use.
+"""
+
+# Exports
+__all__ = []
+
+
+# Imports
+from os.path import dirname
+from pathlib import Path
+from tempfile import mkstemp
+from typing import Any
+
+from jinja2 import Environment, FileSystemLoader, PackageLoader, Template
+
+
+# Globals
+try:
+    _jinja_environment = Environment(
+        loader=FileSystemLoader(dirname(__file__).replace("\\", "/") + "/templates")
+    )
+except ValueError:
+    _jinja_environment = Environment(loader=PackageLoader("gempyor"))
+
+
+# Functions
+def _get_template(name: str) -> Template:
+    """
+    Get a jinja template by name.
+
+    Args:
+        name: The name of the template to pull.
+
+    Returns:
+        A jinja template object corresponding to `name`.
+
+    Examples:
+        >>> _get_template("test_template.j2")
+        <Template 'test_template.j2'>
+    """
+    return _jinja_environment.get_template(name)
+
+
+def _render_template(name: str, data: dict[str, Any]) -> str:
+    """
+    Render a jinja template by name.
+
+    Args:
+        name: The name of the template to pull.
+        data: The data to pass to the template when rendering.
+
+    Returns:
+        The rendered template as a string.
+
+    Examples:
+        >>> _render_template("test_template.j2", {"name": "Bob"})
+        'Hello Bob!'
+    """
+    return _get_template(name).render(data)
+
+
+def _render_template_to_file(name: str, data: dict[str, Any], file: Path) -> None:
+    """
+    Render a jinja template and save to a file.
+
+    Args:
+        name: The name of the template to pull.
+        data: The data to pass to the template when rendering.
+        file: The file to save the rendered template to.
+
+    Examples:
+        >>> from pathlib import Path
+        >>> file = Path("hi.txt")
+        >>> _render_template_to_file("test_template.j2", {"name": "Jane"}, file)
+        >>> file.read_text()
+        'Hello Jane!'
+    """
+    with file.open(mode="w", encoding="utf-8") as f:
+        f.write(_render_template(name, data))
+
+
+def _render_template_to_temp_file(
+    name: str,
+    data: dict[str, Any],
+    suffix: str | None = None,
+    prefix: str | None = None,
+) -> Path:
+    """
+    Render a jinja template and save to a temporary file.
+
+    Args:
+        name: The name of the template to pull.
+        data: The data to pass to the template when rendering.
+        suffix: The suffix of the temporary file, such as an extension. Passed on to
+            `tempfile.mkstemp`.
+        prefix: The prefix of the temporary file. Passed on to `tempfile.mkstemp`.
+
+    Returns:
+        The file containing the rendered template as a `Path` object.
+
+    See Also:
+        [`tempfile.mkstemp`](https://docs.python.org/3/library/tempfile.html#tempfile.mkstemp)
+
+    Examples:
+        >>> file = _render_template_to_temp_file(
+        ...     "test_template.j2", {"name": "John"}, suffix=".txt", prefix="foo_"
+        ... )
+        >>> file
+        PosixPath('/var/folders/2z/h3pc0p7s3ng1tvxrgsw5kr680000gp/T/foo_ocaomg4k.txt')
+        >>> file.read_text()
+        'Hello John!'
+    """
+    _, tmp = mkstemp(suffix=suffix, prefix=prefix, text=True)
+    tmp = Path(tmp)
+    _render_template_to_file(name, data, tmp)
+    return tmp