Doc: misc (#54)

* Link docs

* docstring

* raise

* format

* Remove PEtab process

* Apply suggestions from code review

Co-authored-by: Yannik Schälte <[email protected]>

Co-authored-by: Yannik Schälte <[email protected]>

Author: dweindl

README.md

@@ -34,16 +34,18 @@ Development versions of the PEtab library can be installed using
 When setting up a new parameter estimation problem, the most useful tools will
 be:
 
-  - The **PEtab validator**, which is now automatically installed using Python
-    entrypoints to be available as a shell command from anywhere called
+  - The [PEtab validator](https://petab.readthedocs.io/projects/libpetab-python/en/latest/example/example_petablint.html),
+    which is automatically installed using Python
+    entrypoints to be available as a shell command from anywhere, called
     `petablint`
 
-  - `petab.create_parameter_df` to create the parameter table, once you
-    have set up the model, condition table, observable table and measurement
-    table
+  - [`petab.create_parameter_df`](https://petab.readthedocs.io/projects/libpetab-python/en/latest/build/_autosummary/petab.parameters.html#petab.parameters.create_parameter_df)
+    to create the parameter table, once you have set up the model, 
+    condition table, observable table and measurement table
 
-  - `petab.create_combine_archive` to create a
-    [COMBINE Archive](https://combinearchive.org/index/) from PEtab files
+  - [`petab.create_combine_archive`](https://petab.readthedocs.io/projects/libpetab-python/en/latest/build/_autosummary/petab.core.html#petab.core.create_combine_archive)
+    to create a [COMBINE Archive](https://combinearchive.org/index/) from PEtab
+    files
 
 ## Examples
 

doc/conf.py

@@ -19,7 +19,7 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'PEtab'
+project = 'libpetab-python'
 copyright = '2018, the PEtab developers'
 author = 'PEtab developers'
 

doc/development.rst

@@ -12,7 +12,6 @@
    :caption: About
 
    Changelog <CHANGELOG.md>
-   Development <development>
    how_to_cite
    license
 

doc/index.rst

@@ -363,5 +363,9 @@ def calculate_single_llh(
         nllh = log(2*sigma*m) + abs((log(s)-log(m))/sigma)
     elif noise_distribution == LAPLACE and scale == LOG10:
         nllh = log(2*sigma*m*log(10)) + abs((log10(s)-log10(m))/sigma)
+    else:
+        raise NotImplementedError(
+            "Unsupported combination of noise_distribution and scale "
+            f"specified: {noise_distribution}, {scale}.")
     llh = - nllh
     return llh

petab/calculate.py

@@ -238,7 +238,8 @@ def is_empty(val) -> bool:
 
 
 def create_combine_archive(
-        yaml_file: str, filename: str,
+        yaml_file: str,
+        filename: str,
         family_name: Optional[str] = None,
         given_name: Optional[str] = None,
         email: Optional[str] = None,
@@ -249,6 +250,7 @@ def create_combine_archive(
 
     Arguments:
         yaml_file: Path to PEtab YAML file
+        filename: Destination file name
         family_name: Family name of archive creator
         given_name: Given name of archive creator
         email: E-mail address of archive creator

petab/core.py

@@ -307,8 +307,8 @@ def assert_all_parameters_present_in_parameter_df(
 def assert_measured_observables_defined(
         measurement_df: pd.DataFrame,
         observable_df: pd.DataFrame) -> None:
-    """Check if all observables in the measurement table have been defined in the
-    observable table
+    """Check if all observables in the measurement table have been defined in
+    the observable table
 
     Arguments:
         measurement_df: PEtab measurement table