Merge pull request #269 from CovertLab/superhelical-fix

Handle removed replisomes in superhelical density calculations

.pre-commit-config.yaml

@@ -0,0 +1,12 @@
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.8.3
+  hooks:
+    # Run the linter.
+    - id: ruff
+      types_or: [ python, pyi ]
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format
+      types_or: [ python, pyi ]

README.md

@@ -71,6 +71,19 @@ finishes, close and reopen your terminal before continuing with the
 > **Tip:** If any step in the `nextflow` installation fails,
 > try rerunning a few times to see if that fixes the issue.
 
+If you are installing the model for active development, we strongly
+recommend that you also install the development dependencies using:
+
+    uv sync --frozen --extra dev
+
+After that, you can run ``uv run pre-commit install`` to install
+a pre-commit hook that will run the ``ruff`` linter and formatter
+before all of your commits.
+
+The development dependencies also include ``pytest``, which lets
+you run the test suite, and ``mypy``, which can be invoked to
+perform static type checking.
+
 ## Test Installation
 
 To test your installation, from the top-level of the cloned repository, invoke:

doc/stores.rst

@@ -336,9 +336,7 @@ molecule). All unique molecules will have the following named fields:
         generate the new unique indices. If you need to reference the unique
         indices of new molecules in the same process AND timestep in which they
         are generated, see :py:meth:`ecoli.library.schema.create_unique_indices`.
-        Note that unique indices are only unique for a cell and its ancestors. For
-        example, two daughter cells from the same parent cell will have conflicting
-        unique indices.
+        Note that unique indices are only unique within a single cell.
     2. ``_entryState`` (:py:attr:`numpy.int8`): 1 for active row, 0 for inactive row
         When unique molecules are deleted (e.g. RNA degradation), all of their data, 
         including the ``_entryState`` field, is set to 0. When unique molecues are 
@@ -352,6 +350,17 @@ molecule). All unique molecules will have the following named fields:
         changing protein mass of the polypeptide associated with an actively 
         translating ribosome.
 
+.. note::
+    Unique molecules are instances of :py:class:`~ecoli.library.schema.MetadataArray`,
+    a subclass of Numpy arrays that adds a ``metadata`` attribute. This attribute
+    is used to store the next unique index to be assigned to a new unique molecule.
+    If you wish to add a custom unique molecule type, after you have
+    created a structured Numpy array with at least the above attributes,
+    create a :py:class:`~ecoli.library.schema.MetadataArray` instance from it using
+    ``MetadataArray(array, next_unique_index)``, where ``array`` is your structured
+    Numpy array and ``next_unique_index`` is the next unique index to be assigned.
+
+
 Initialization
 ==============
 See :ref:`initialization`.

doc/workflows.rst

@@ -679,7 +679,8 @@ is a list workflow behaviors enabled in our model to handle unexpected errors.
 - If you realize that a code issue is the cause of job failure(s), stop
   the workflow run if it is not already (e.g. ``control + c``, ``scancel``,
   etc.), make the necessary code fixes, and rerun :py:mod:`runscripts.workflow`
-  with the same configuration JSON and the ``--resume`` command-line argument.
+  with the same configuration JSON and the ``--resume`` command-line argument,
+  supplying the experiment ID (with time suffix if using ``suffix_time`` option).
   Nextflow will intelligently resume workflow execution from the last successful
   job in each chain of job dependencies (e.g. generation 7 of a cell lineage
   depends on generation 6, :py:mod:`runscripts.create_variants` depends on

ecoli/library/initial_conditions.py

@@ -1240,10 +1240,7 @@ def initialize_transcription(
     unique_molecules["RNA"] = np.concatenate((partial_rnas, full_rnas))
     # Have to recreate unique indices or else there will be conflicts between
     # full and partial RNAs
-    unique_mol_names = list(
-        sim_data.internal_state.unique_molecule.unique_molecule_definitions.keys()
-    )
-    unique_prefix = unique_mol_names.index("RNA") << 59
+    unique_prefix = np.min(unique_molecules["RNA"]["unique_index"])
     unique_molecules["RNA"]["unique_index"] = np.arange(
         unique_prefix, unique_prefix + len(unique_molecules["RNA"])
     )

ecoli/library/schema.py

@@ -116,6 +116,18 @@ class MetadataArray(np.ndarray):
     def __new__(cls, input_array, metadata=None):
         # Input array should be an array instance
         obj = np.asarray(input_array).view(cls)
+        # Ensure unique_index field exists and is unique
+        if "unique_index" in obj.dtype.names:
+            if "_entryState" in obj.dtype.names:
+                unique_indices = obj["unique_index"][obj["_entryState"].view(np.bool_)]
+                if len(unique_indices) != len(set(unique_indices)):
+                    raise ValueError(
+                        "All elements in the 'unique_index' field must be unique."
+                    )
+            else:
+                raise ValueError("Input array must have an '_entryState' field.")
+        else:
+            raise ValueError("Input array must have a 'unique_index' field.")
         obj.metadata = metadata
         return obj