From b13ba46120b7ab656aa1527f249869f1cd95920b Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Mon, 16 Dec 2024 12:43:34 -0800
Subject: [PATCH 1/8] Fix workflow resumption with suffix_time

---
 doc/workflows.rst      |  3 ++-
 runscripts/workflow.py | 23 ++++++++++++++---------
 2 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/doc/workflows.rst b/doc/workflows.rst
index 02f9fb68b..023250b78 100644
--- a/doc/workflows.rst
+++ b/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
diff --git a/runscripts/workflow.py b/runscripts/workflow.py
index 91fb4140f..53235266a 100644
--- a/runscripts/workflow.py
+++ b/runscripts/workflow.py
@@ -311,9 +311,11 @@ def main():
     )
     parser.add_argument(
         "--resume",
-        action="store_true",
-        default=False,
-        help="Resume last run workflow.",
+        type=str,
+        default=None,
+        help="Resume workflow with given experiment ID. The experiment ID must "
+        "match the supplied configuration file and if suffix_time was used, must "
+        "contain the full time suffix (suffix_time will not be applied again).",
     )
     args = parser.parse_args()
     with open(config_file, "r") as f:
@@ -335,11 +337,14 @@ def main():
     experiment_id = config["experiment_id"]
     if experiment_id is None:
         raise RuntimeError("No experiment ID was provided.")
-    if config["suffix_time"]:
+    if args.resume is not None:
+        experiment_id = args.resume
+        config["experiment_id"] = args.resume
+    elif config["suffix_time"]:
         current_time = datetime.now().strftime("%Y%m%d-%H%M%S")
         experiment_id = experiment_id + "_" + current_time
         config["experiment_id"] = experiment_id
-        config["suffix_time"] = False
+    config["suffix_time"] = False
     # Special characters are messy so do not allow them
     if experiment_id != parse.quote_plus(experiment_id):
         raise TypeError(
@@ -370,7 +375,7 @@ def main():
     final_config_uri = os.path.join(out_uri, "workflow_config.json")
     with open(temp_config_path, "w") as f:
         json.dump(config, f)
-    if not args.resume:
+    if args.resume is None:
         copy_to_filesystem(temp_config_path, final_config_path, filesystem)
 
     nf_config = os.path.join(os.path.dirname(__file__), "nextflow", "config.template")
@@ -471,7 +476,7 @@ def main():
     workflow_path = os.path.join(out_uri, "main.nf")
 
     config_path = os.path.join(out_uri, "nextflow.config")
-    if not args.resume:
+    if args.resume is None:
         copy_to_filesystem(local_workflow, os.path.join(outdir, "main.nf"), filesystem)
         copy_to_filesystem(
             local_config, os.path.join(outdir, "nextflow.config"), filesystem
@@ -497,7 +502,7 @@ def main():
                 report_path,
                 "-work-dir",
                 workdir,
-                "-resume" if args.resume else "",
+                "-resume" if args.resume is not None else "",
             ],
             check=True,
         )
@@ -511,7 +516,7 @@ def main():
 #SBATCH --mem=4GB
 #SBATCH --partition=mcovert
 nextflow -C {config_path} run {workflow_path} -profile {nf_profile} \
-    -with-report {report_path} -work-dir {workdir} {"-resume" if args.resume else ""}
+    -with-report {report_path} -work-dir {workdir} {"-resume" if args.resume is not None else ""}
 """)
         copy_to_filesystem(
             batch_script, os.path.join(outdir, "nextflow_job.sh"), filesystem

From 2e26c55a33b6743e90dfa91522ea9033b8ca92bc Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Mon, 16 Dec 2024 14:25:59 -0800
Subject: [PATCH 2/8] Copy publish mode allows task caching when resuming
 workflow

---
 runscripts/nextflow/analysis.nf | 10 +++++-----
 runscripts/nextflow/template.nf |  2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/runscripts/nextflow/analysis.nf b/runscripts/nextflow/analysis.nf
index 6c5735d7b..93479424a 100644
--- a/runscripts/nextflow/analysis.nf
+++ b/runscripts/nextflow/analysis.nf
@@ -1,5 +1,5 @@
 process analysisSingle {
-    publishDir "${params.publishDir}/${params.experimentId}/analyses/variant=${variant}/lineage_seed=${lineage_seed}/generation=${generation}/agent_id=${agent_id}", mode: "move"
+    publishDir "${params.publishDir}/${params.experimentId}/analyses/variant=${variant}/lineage_seed=${lineage_seed}/generation=${generation}/agent_id=${agent_id}", mode: "copy"
 
     tag "variant=${variant}/lineage_seed=${lineage_seed}/generation=${generation}/agent_id=${agent_id}"
 
@@ -49,7 +49,7 @@ process analysisSingle {
 }
 
 process analysisMultiDaughter {
-    publishDir "${params.publishDir}/${params.experimentId}/analyses/variant=${variant}/lineage_seed=${lineage_seed}/generation=${generation}", mode: "move"
+    publishDir "${params.publishDir}/${params.experimentId}/analyses/variant=${variant}/lineage_seed=${lineage_seed}/generation=${generation}", mode: "copy"
 
     tag "variant=${variant}/lineage_seed=${lineage_seed}/generation=${generation}"
 
@@ -97,7 +97,7 @@ process analysisMultiDaughter {
 }
 
 process analysisMultiGeneration {
-    publishDir "${params.publishDir}/${params.experimentId}/analyses/variant=${variant}/lineage_seed=${lineage_seed}", mode: "move"
+    publishDir "${params.publishDir}/${params.experimentId}/analyses/variant=${variant}/lineage_seed=${lineage_seed}", mode: "copy"
 
     tag "variant=${variant}/lineage_seed=${lineage_seed}"
 
@@ -143,7 +143,7 @@ process analysisMultiGeneration {
 }
 
 process analysisMultiSeed {
-    publishDir "${params.publishDir}/${params.experimentId}/analyses/variant=${variant}", mode: "move"
+    publishDir "${params.publishDir}/${params.experimentId}/analyses/variant=${variant}", mode: "copy"
 
     tag "variant=${variant}"
 
@@ -187,7 +187,7 @@ process analysisMultiSeed {
 }
 
 process analysisMultiVariant {
-    publishDir "${params.publishDir}/${params.experimentId}/analyses", mode: "move"
+    publishDir "${params.publishDir}/${params.experimentId}/analyses", mode: "copy"
 
     label "short"
 
diff --git a/runscripts/nextflow/template.nf b/runscripts/nextflow/template.nf
index 7118ba0d0..4eb48db4f 100644
--- a/runscripts/nextflow/template.nf
+++ b/runscripts/nextflow/template.nf
@@ -26,7 +26,7 @@ process runParca {
 }
 
 process analysisParca {
-    publishDir "${params.publishDir}/${params.experimentId}/parca/analysis", mode: "move"
+    publishDir "${params.publishDir}/${params.experimentId}/parca/analysis", mode: "copy"
 
     label "short"
 

From 0629fb38406a313ce937254d8d23f4aca081a2ca Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Mon, 16 Dec 2024 14:26:44 -0800
Subject: [PATCH 3/8] Handle replisome removal in superhelical density

---
 ecoli/processes/chromosome_structure.py | 564 ++++++++++++++++++++----
 migration/migration_utils.py            |   9 +-
 2 files changed, 489 insertions(+), 84 deletions(-)

diff --git a/ecoli/processes/chromosome_structure.py b/ecoli/processes/chromosome_structure.py
index 4b41e52dc..217371f88 100644
--- a/ecoli/processes/chromosome_structure.py
+++ b/ecoli/processes/chromosome_structure.py
@@ -99,6 +99,7 @@ class ChromosomeStructure(Step):
         "mature_rna_end_positions": [],
         "mature_rna_nt_counts": [],
         "unprocessed_rna_index_mapping": {},
+        "removed_replisome_index": -2,
         "time_step": 1.0,
     }
 
@@ -119,6 +120,7 @@ def __init__(self, parameters=None):
             "relaxed_DNA_base_pairs_per_turn"
         ]
         self.terC_index = self.parameters["terC_index"]
+        self.removed_replisome_index = self.parameters["removed_replisome_index"]
 
         self.n_mature_rnas = self.parameters["n_mature_rnas"]
         self.mature_rna_ids = self.parameters["mature_rna_ids"]
@@ -164,6 +166,8 @@ def ports_schema(self):
                             np.zeros(self.n_TUs, np.int64),
                             self.rna_ids,
                         ),
+                        "n_empty_fork_collisions": 0,
+                        "empty_fork_collision_coordinates": [],
                     }
                 )
             },
@@ -334,14 +338,14 @@ def get_removed_molecules_mask(domain_indexes, coordinates):
 
                 # Domain has no active replisomes
                 else:
-                    # Domain has child domains (has finished replicating)
-                    if (
-                        child_domains[all_chromosome_domain_indexes == domain_index, 0]
-                        != self.no_child_place_holder
-                    ):
+                    children_of_domain = child_domains[
+                        all_chromosome_domain_indexes == domain_index
+                    ]
+                    # Child domains are full chromosomes (domain has finished replicating)
+                    if np.all(np.isin(children_of_domain, mother_domain_indexes)):
                         # Remove all molecules on this domain
                         domain_mask = domain_indexes == domain_index
-                    # Domain has not started replication
+                    # Domain has not started replication or replication was interrupted
                     else:
                         continue
 
@@ -363,12 +367,6 @@ def get_removed_molecules_mask(domain_indexes, coordinates):
             DnaA_box_domain_indexes, DnaA_box_coordinates
         )
 
-        # Get attribute arrays of remaining RNAPs
-        remaining_RNAPs_mask = np.logical_not(removed_RNAPs_mask)
-        remaining_RNAP_domain_indexes = RNAP_domain_indexes[remaining_RNAPs_mask]
-        remaining_RNAP_coordinates = RNAP_coordinates[remaining_RNAPs_mask]
-        remaining_RNAP_unique_indexes = RNAP_unique_indexes[remaining_RNAPs_mask]
-
         # Build masks for head-on and co-directional collisions between RNAPs
         # and replication forks
         RNAP_headon_collision_mask = np.logical_and(
@@ -434,6 +432,9 @@ def get_removed_molecules_mask(domain_indexes, coordinates):
             all_new_segment_domain_indexes = np.array([], dtype=np.int32)
             all_new_linking_numbers = np.array([], dtype=np.float64)
 
+            # Iteratively tally RNAPs that were removed due to collisions with
+            # replication forks with or without replisomes on each domain
+            removed_RNAP_masks_all_domains = np.full_like(removed_RNAPs_mask, False)
             for domain_index in np.unique(all_chromosome_domain_indexes):
                 # Skip domains that have completed replication
                 if np.all(domain_index < mother_domain_indexes):
@@ -442,11 +443,14 @@ def get_removed_molecules_mask(domain_indexes, coordinates):
                 domain_spans_oriC = domain_index in origin_domain_indexes
                 domain_spans_terC = domain_index in mother_domain_indexes
 
-                # Get masks for segments and RNAPs in this domain
-                segments_domain_mask = segment_domain_indexes == domain_index
-                RNAP_domain_mask = remaining_RNAP_domain_indexes == domain_index
+                # Parse attributes of remaining RNAPs in this domain
+                RNAPs_domain_mask = RNAP_domain_indexes == domain_index
+                RNAP_coordinates_this_domain = RNAP_coordinates[RNAPs_domain_mask]
+                RNAP_unique_indexes_this_domain = RNAP_unique_indexes[RNAPs_domain_mask]
+                domain_remaining_RNAPs_mask = ~removed_RNAPs_mask[RNAPs_domain_mask]
 
                 # Parse attributes of segments in this domain
+                segments_domain_mask = segment_domain_indexes == domain_index
                 boundary_molecule_indexes_this_domain = boundary_molecule_indexes[
                     segments_domain_mask, :
                 ]
@@ -455,29 +459,59 @@ def get_removed_molecules_mask(domain_indexes, coordinates):
                 ]
                 linking_numbers_this_domain = linking_numbers[segments_domain_mask]
 
-                # Parse attributes of remaining RNAPs in this domain
-                new_molecule_coordinates_this_domain = remaining_RNAP_coordinates[
-                    RNAP_domain_mask
-                ]
-                new_molecule_indexes_this_domain = remaining_RNAP_unique_indexes[
-                    RNAP_domain_mask
-                ]
-
+                new_molecule_coordinates_this_domain = np.array([], dtype=np.int64)
+                new_molecule_indexes_this_domain = np.array([], dtype=np.int64)
                 # Append coordinates and indexes of replisomes on this domain,
                 # if any
                 if not domain_spans_oriC:
                     replisome_domain_mask = replisome_domain_indexes == domain_index
+                    replisome_coordinates_this_domain = replisome_coordinates[
+                        replisome_domain_mask
+                    ]
+                    replisome_molecule_indexes_this_domain = replisome_unique_indexes[
+                        replisome_domain_mask
+                    ]
+
+                    # If one or more replisomes was removed in the last time step,
+                    # use the last known location and molecule index.
+                    if len(replisome_molecule_indexes_this_domain) != 2:
+                        assert len(replisome_molecule_indexes_this_domain) < 2
+                        (
+                            replisome_coordinates_this_domain,
+                            replisome_molecule_indexes_this_domain,
+                        ) = get_last_known_replisome_data(
+                            boundary_coordinates_this_domain,
+                            boundary_molecule_indexes_this_domain,
+                            replisome_coordinates_this_domain,
+                            replisome_molecule_indexes_this_domain,
+                        )
+                        # Assume that RNAPs that run into a replication fork
+                        # are removed even if there is no replisome
+                        RNAPs_on_forks = np.isin(
+                            RNAP_coordinates_this_domain,
+                            replisome_coordinates_this_domain,
+                        )
+                        domain_remaining_RNAPs_mask = np.logical_and(
+                            domain_remaining_RNAPs_mask, ~RNAPs_on_forks
+                        )
+                        full_removed_RNAPs_mask = np.full_like(
+                            removed_RNAPs_mask, False
+                        )
+                        full_removed_RNAPs_mask[RNAPs_domain_mask] = RNAPs_on_forks
+                        removed_RNAP_masks_all_domains = np.logical_or(
+                            removed_RNAP_masks_all_domains, full_removed_RNAPs_mask
+                        )
 
                     new_molecule_coordinates_this_domain = np.concatenate(
                         (
                             new_molecule_coordinates_this_domain,
-                            replisome_coordinates[replisome_domain_mask],
+                            replisome_coordinates_this_domain,
                         )
                     )
                     new_molecule_indexes_this_domain = np.concatenate(
                         (
                             new_molecule_indexes_this_domain,
-                            replisome_unique_indexes[replisome_domain_mask],
+                            replisome_molecule_indexes_this_domain,
                         )
                     )
 
@@ -490,20 +524,81 @@ def get_removed_molecules_mask(domain_indexes, coordinates):
                     replisome_parent_domain_mask = (
                         replisome_domain_indexes == parent_domain_index
                     )
+                    replisome_coordinates_parent_domain = replisome_coordinates[
+                        replisome_parent_domain_mask
+                    ]
+                    replisome_molecule_indexes_parent_domain = replisome_unique_indexes[
+                        replisome_parent_domain_mask
+                    ]
+
+                    # If one or more replisomes was removed in the last time step,
+                    # use the last known location and molecule index.
+                    if len(replisome_molecule_indexes_parent_domain) != 2:
+                        assert len(replisome_molecule_indexes_parent_domain) < 2
+                        # Parse attributes of segments in parent domain
+                        parent_segments_domain_mask = (
+                            segment_domain_indexes == parent_domain_index
+                        )
+                        boundary_molecule_indexes_parent_domain = (
+                            boundary_molecule_indexes[parent_segments_domain_mask, :]
+                        )
+                        boundary_coordinates_parent_domain = boundary_coordinates[
+                            parent_segments_domain_mask, :
+                        ]
+                        (
+                            replisome_coordinates_parent_domain,
+                            replisome_molecule_indexes_parent_domain,
+                        ) = get_last_known_replisome_data(
+                            boundary_coordinates_parent_domain,
+                            boundary_molecule_indexes_parent_domain,
+                            replisome_coordinates_parent_domain,
+                            replisome_molecule_indexes_parent_domain,
+                        )
+                        # Assume that RNAPs that run into a replication fork
+                        # are removed even if there is no replisome
+                        RNAPs_on_forks = np.isin(
+                            RNAP_coordinates_this_domain,
+                            replisome_coordinates_parent_domain,
+                        )
+                        domain_remaining_RNAPs_mask = np.logical_and(
+                            domain_remaining_RNAPs_mask, ~RNAPs_on_forks
+                        )
+                        full_removed_RNAPs_mask = np.full_like(
+                            removed_RNAPs_mask, False
+                        )
+                        full_removed_RNAPs_mask[RNAPs_domain_mask] = RNAPs_on_forks
+                        removed_RNAP_masks_all_domains = np.logical_or(
+                            removed_RNAP_masks_all_domains, full_removed_RNAPs_mask
+                        )
 
                     new_molecule_coordinates_this_domain = np.concatenate(
                         (
                             new_molecule_coordinates_this_domain,
-                            replisome_coordinates[replisome_parent_domain_mask],
+                            replisome_coordinates_parent_domain,
                         )
                     )
                     new_molecule_indexes_this_domain = np.concatenate(
                         (
                             new_molecule_indexes_this_domain,
-                            replisome_unique_indexes[replisome_parent_domain_mask],
+                            replisome_molecule_indexes_parent_domain,
                         )
                     )
 
+                # Add remaining RNAPs in this domain after accounting for removals
+                # due to collisions with replication forks
+                new_molecule_coordinates_this_domain = np.concatenate(
+                    (
+                        new_molecule_coordinates_this_domain,
+                        RNAP_coordinates_this_domain[domain_remaining_RNAPs_mask],
+                    )
+                )
+                new_molecule_indexes_this_domain = np.concatenate(
+                    (
+                        new_molecule_indexes_this_domain,
+                        RNAP_unique_indexes_this_domain[domain_remaining_RNAPs_mask],
+                    )
+                )
+
                 # If there are no molecules left on this domain, continue
                 if len(new_molecule_indexes_this_domain) == 0:
                     continue
@@ -564,6 +659,25 @@ def get_removed_molecules_mask(domain_indexes, coordinates):
                 }
             )
 
+            # Figure out if any additional RNAPs were removed due to collisions with
+            # replication forks where there were no replisomes
+            empty_fork_RNAP_collision_mask = np.logical_and(
+                removed_RNAP_masks_all_domains,
+                np.logical_not(
+                    np.logical_or(
+                        RNAP_headon_collision_mask, RNAP_codirectional_collision_mask
+                    )
+                ),
+            )
+            update["listeners"]["rnap_data"].update(
+                {
+                    "n_empty_fork_collisions": empty_fork_RNAP_collision_mask.sum(),
+                    "empty_fork_collision_coordinates": RNAP_coordinates[
+                        empty_fork_RNAP_collision_mask
+                    ],
+                }
+            )
+
         # Get mask for RNAs that are transcribed from removed RNAPs
         removed_RNAs_mask = np.isin(
             RNA_RNAP_indexes, RNAP_unique_indexes[removed_RNAPs_mask]
@@ -1128,10 +1242,73 @@ def _compute_new_segment_attributes(
         }
 
 
-def test_superhelical_bug():
+def get_last_known_replisome_data(
+    boundary_coordinates,
+    boundary_molecule_indexes,
+    replisome_coordinates,
+    replisome_molecule_indexes,
+):
+    # Sort old boundary coordinates and molecule indexes to find first index
+    # where left boundary is non-negative
+    boundary_coordinates_argsort = np.argsort(boundary_coordinates[:, 0])
+    boundary_coordinates_sorted = boundary_coordinates[boundary_coordinates_argsort]
+    boundary_molecule_indexes_sorted = boundary_molecule_indexes[
+        boundary_coordinates_argsort
+    ]
+    replisome_index = np.argmax(boundary_coordinates_sorted[:, 0] >= 0)
+    # If positive coordinate replisome still exists, add
+    # last known info on negative coordinate replisome.
+    if np.any(replisome_coordinates > 0):
+        replisome_coordinates = np.insert(
+            replisome_coordinates,
+            0,
+            boundary_coordinates_sorted[replisome_index - 1, 1],
+        )
+        replisome_molecule_indexes = np.insert(
+            replisome_molecule_indexes,
+            0,
+            boundary_molecule_indexes_sorted[replisome_index - 1, 1],
+        )
+    # If negative coordinate replisome still exists, add
+    # last known info on positive coordinate replisome.
+    elif np.any(replisome_coordinates < 0):
+        replisome_coordinates = np.insert(
+            replisome_coordinates, 0, boundary_coordinates_sorted[replisome_index, 0]
+        )
+        replisome_molecule_indexes = np.insert(
+            replisome_molecule_indexes,
+            0,
+            boundary_molecule_indexes_sorted[replisome_index, 0],
+        )
+    # If neither replisomes exist, use last known info on both.
+    else:
+        replisome_coordinates = np.array(
+            [
+                boundary_coordinates_sorted[replisome_index - 1, 1],
+                boundary_coordinates_sorted[replisome_index, 0],
+            ]
+        )
+        replisome_molecule_indexes = np.array(
+            [
+                boundary_molecule_indexes_sorted[replisome_index - 1, 1],
+                boundary_molecule_indexes_sorted[replisome_index, 0],
+            ]
+        )
+
+    return replisome_coordinates, replisome_molecule_indexes
+
+
+def test_superhelical_removal_sim():
     """
-    Test that ChromosomeStructure correctly handles edge case where RNAP and replisome
-    share the same genomic coordinates.
+    Run a single time step simulation of :py:class:`~.ChromosomeStructure`
+    that tests some edge cases in superhelical density calculations. Start with
+    a chromosome that has four active replication forks for a total of 4 replisomes
+    and 5 chromosome domains. There are 4 RNAPs per domain and 1 to 2 of those
+    will be intentionally placed at the same coordinates as a replisome per domain.
+    They should be removed, causing some segment boundaries to be redefined.
+    Additionally, 3 of the replisomes will be removed. This should be detected
+    and superhelical density calculations should still work using the last known
+    information for the removed replisomes.
     """
     # Get topology for UniqueUpdate Steps
     unique_topology = TOPOLOGY.copy()
@@ -1158,7 +1335,7 @@ def generate_processes(self, config):
                         "water": "WATER[c]",
                         "mature_rna_ids": ["alaT-tRNA[c]"],
                         "fragmentBases": ["polymerized_ATP[c]"],
-                        "replichore_lengths": [2000, 2000],
+                        "replichore_lengths": [100000, 100000],
                         "calculate_superhelical_densities": True,
                     }
                 ),
@@ -1168,10 +1345,6 @@ def generate_processes(self, config):
 
         def generate_topology(self, config):
             return {
-                "rnap_remover": {
-                    "active_RNAPs": ("unique", "active_RNAP"),
-                    "global_time": ("global_time",),
-                },
                 "chromosome_structure": TOPOLOGY,
                 "unique_update": unique_topology,
                 "global_clock": {
@@ -1193,46 +1366,158 @@ def generate_flow(self, config):
         unique_mol.flags.writeable = True
         unique_mol["_entryState"] = 0
         unique_mol.flags.writeable = False
-    # Set up chromosome domain 1
+    # Set up a single full chromosome
     full_chromosomes = template_initial_state["unique"]["full_chromosome"]
     full_chromosomes.flags.writeable = True
     full_chromosomes["_entryState"][0] = 1
-    full_chromosomes["domain_index"][0] = 1
+    full_chromosomes["domain_index"][0] = 0
     full_chromosomes.flags.writeable = False
-    chromosome_domains = template_initial_state["unique"]["chromosome_domain"]
+    # Set up chromosome domains
+    chromosome_domains, replisome_idx = get_free_indices(
+        template_initial_state["unique"]["chromosome_domain"], 5
+    )
     chromosome_domains.flags.writeable = True
-    chromosome_domains["_entryState"][0] = 1
-    chromosome_domains["domain_index"][0] = 1
-    chromosome_domains["child_domains"][0] = [-1, -1]
+    chromosome_domains["_entryState"][replisome_idx] = 1
+    chromosome_domains["domain_index"][replisome_idx] = np.arange(5)
+    chromosome_domains["child_domains"][replisome_idx] = [
+        [1, 2],
+        [3, 4],
+        [-1, -1],
+        [-1, -1],
+        [-1, -1],
+    ]
     chromosome_domains.flags.writeable = False
-    # Add two replisomes at -1000 and 1000
-    active_replisomes = template_initial_state["unique"]["active_replisome"]
+    template_initial_state["unique"]["chromosome_domain"] = chromosome_domains
+    # Set up 1 oriC per domain that is not actively replicating
+    oriCs, oriC_idx = get_free_indices(template_initial_state["unique"]["oriC"], 3)
+    oriCs.flags.writeable = True
+    oriCs["_entryState"][oriC_idx] = 1
+    oriCs["domain_index"][oriC_idx] = [2, 3, 4]
+    oriCs.flags.writeable = False
+    template_initial_state["unique"]["oriC"] = oriCs
+    # Set up replisome for actively replicating domain
+    # Notice that the replisomes previously at 45000, 20000, and -20000
+    # when the chromosomal segment data below was tabulated are removed
+    active_replisomes, replisome_idx = get_free_indices(
+        template_initial_state["unique"]["active_replisome"], 1
+    )
     active_replisomes.flags.writeable = True
-    active_replisomes["_entryState"][:2] = 1
-    active_replisomes["domain_index"][:2] = 1
-    active_replisomes["coordinates"][:2] = [-1000, 1000]
-    active_replisomes["unique_index"][:2] = [1, 2]
+    active_replisomes["_entryState"][replisome_idx] = 1
+    active_replisomes["domain_index"][replisome_idx] = 0
+    active_replisomes["coordinates"][replisome_idx] = -50000
+    active_replisomes["unique_index"][replisome_idx] = 0
     active_replisomes.flags.writeable = False
-    # Add four RNAPs: two that coincide with replisomes, two that do not
+    template_initial_state["unique"]["active_replisome"] = active_replisomes
+    # Set up 4 RNAPs per domain, some of which will intentionally have
+    # the same coordinates as replisomes (either active or removed)
     active_RNAP = template_initial_state["unique"]["active_RNAP"]
     active_RNAP.flags.writeable = True
-    active_RNAP["_entryState"][:4] = 1
-    active_RNAP["domain_index"][:4] = 1
-    active_RNAP["coordinates"][:4] = [-1500, -1000, 1000, 1500]
-    active_RNAP["is_forward"][:4] = [True, True, True, True]
-    active_RNAP["unique_index"][:4] = [3, 4, 5, 6]
+    coordinates_per_domain = [
+        [-65000, -50000, 60000, 75000],
+        [-40000, -26000, 25000, 35000],
+        [-30000, -10000, 20000, 40000],
+        [-20000, -15000, 10000, 15000],
+    ]
+    for i in range(4):
+        active_RNAP["_entryState"][i * 4 : (i + 1) * 4] = 1
+        active_RNAP["domain_index"][i * 4 : (i + 1) * 4] = i
+        active_RNAP["is_forward"][i * 4 : (i + 1) * 4] = True
+        active_RNAP["coordinates"][i * 4 : (i + 1) * 4] = coordinates_per_domain[i]
+        active_RNAP["unique_index"][i * 4 : (i + 1) * 4] = np.arange(
+            4 + i * 4, 4 + (i + 1) * 4
+        )
+    # Special domain 4 that will be left with no molecules
+    active_RNAP["_entryState"][16:18] = 1
+    active_RNAP["domain_index"][16:18] = 4
+    active_RNAP["is_forward"][16:18] = True
+    active_RNAP["coordinates"][16:18] = [-20000, 20000]
+    active_RNAP["unique_index"][16:18] = np.arange(20, 22)
     active_RNAP.flags.writeable = False
-    # Add chromosomal segments between replisome and RNAPs on either side
-    # of origin of replication (coordinates offset from current timestep)
-    chromosomal_segments, _ = get_free_indices(
-        template_initial_state["unique"]["chromosomal_segment"], 2
+    # Construct chromosomal segments by domain
+    # Assume that RNAPs have advanced 1000 bp from their initial coordinates
+    # and replisomes have advanced 5000 bp
+    boundary_coordinates = []
+    boundary_molecule_indexes = []
+    domain_index = []
+    linking_number = []
+    # Segments for domain 0
+    # - Includes replisome at 45000 (index 1) that will be removed
+    # - Includes RNAP (index 5) that will conflict with replisome at -50000 (index 0)
+    boundary_coordinates.extend(
+        [[-64000, -49000], [-49000, -45000], [45000, 59000], [59000, 74000]]
+    )
+    boundary_molecule_indexes.extend([[4, 5], [5, 0], [1, 6], [6, 7]])
+    domain_index.extend([0, 0, 0, 0])
+    linking_number.extend([1, 1, 1, 1])
+    # Segments for domain 1
+    # - Includes replisome at 20000 (index 2) that will be removed
+    # - Includes replisome at -20000 (index 3) that will be removed
+    # - Parent domain replisome at 45000 (index 1) will be removed
+    boundary_coordinates.extend(
+        [
+            [-45000, -39000],
+            [-39000, -25000],
+            [-25000, -20000],
+            [20000, 24000],
+            [24000, 34000],
+            [34000, 45000],
+        ]
+    )
+    boundary_molecule_indexes.extend(
+        [[0, 8], [8, 9], [9, 3], [2, 10], [10, 11], [11, 1]]
+    )
+    domain_index.extend([1, 1, 1, 1, 1, 1])
+    linking_number.extend([1, 1, 1, 1, 1, 1])
+    # Segments for domain 2
+    # - Parent domain replisome at 45000 (index 1) will be removed
+    boundary_coordinates.extend(
+        [
+            [-45000, -29000],
+            [-29000, -9000],
+            [-9000, 19000],
+            [19000, 39000],
+            [39000, 45000],
+        ]
+    )
+    boundary_molecule_indexes.extend([[0, 12], [12, 13], [13, 14], [14, 15], [15, 1]])
+    domain_index.extend([2, 2, 2, 2, 2])
+    linking_number.extend([1, 1, 1, 1, 1])
+    # Segments for domain 3
+    # - Includes RNAP (index 16) that will conflict with replisome that will
+    # be removed at -20000 (index 3)
+    # - Includes replisome at 20000 (index 2) that will be removed
+    boundary_coordinates.extend(
+        [
+            [-20000, -19000],
+            [-19000, -14000],
+            [-14000, 9000],
+            [9000, 14000],
+            [14000, 20000],
+        ]
+    )
+    boundary_molecule_indexes.extend([[3, 16], [16, 17], [17, 18], [18, 19], [19, 2]])
+    domain_index.extend([3, 3, 3, 3, 3])
+    linking_number.extend([1, 1, 1, 1, 1])
+    # Segments for domain 4
+    # - Includes RNAP (index 20) that will conflict with replisome that will
+    # be removed at -20000 (index 3)
+    # - Includes RNAP (index 23) that will conflict with replisome that will
+    # be removed at 20000 (index 2)
+    boundary_coordinates.extend([[-20000, -19000], [-19000, 19000], [19000, 20000]])
+    boundary_molecule_indexes.extend([[3, 20], [20, 21], [21, 2]])
+    domain_index.extend([4, 4, 4])
+    linking_number.extend([1, 1, 1])
+    chromosomal_segments, segment_idx = get_free_indices(
+        template_initial_state["unique"]["chromosomal_segment"], len(linking_number)
     )
     chromosomal_segments.flags.writeable = True
-    chromosomal_segments["_entryState"][:2] = 1
-    chromosomal_segments["boundary_coordinates"][:2] = [[-1400, -800], [800, 1400]]
-    chromosomal_segments["boundary_molecule_indexes"][:2] = [[3, 1], [2, 6]]
-    chromosomal_segments["domain_index"][:2] = 1
-    chromosomal_segments["linking_number"][:2] = 1
+    chromosomal_segments["_entryState"][segment_idx] = 1
+    chromosomal_segments["boundary_coordinates"][segment_idx] = boundary_coordinates
+    chromosomal_segments["boundary_molecule_indexes"][segment_idx] = (
+        boundary_molecule_indexes
+    )
+    chromosomal_segments["domain_index"][segment_idx] = domain_index
+    chromosomal_segments["linking_number"][segment_idx] = linking_number
     chromosomal_segments.flags.writeable = False
     template_initial_state["unique"]["chromosomal_segment"] = chromosomal_segments
     # Since unique numpy updater is an class method, internal
@@ -1250,30 +1535,145 @@ def generate_flow(self, config):
     )
     engine.update(1)
     state = engine.state.get_value()
-    # Check that conflicting RNAPs were removed
-    active_RNAPs = state["unique"]["active_RNAP"][
-        state["unique"]["active_RNAP"]["_entryState"].view(np.bool_)
-    ]
-    assert len(active_RNAPs) == 2
-    assert np.all(active_RNAPs["domain_index"] == 1)
-    assert np.all(active_RNAPs["coordinates"] == np.array([-1500, 1500]))
-    assert np.all(active_RNAPs["unique_index"] == np.array([3, 6]))
-    # Check that chromosomal segments were added for the span between
-    # each replisome and terC in addition to the existing ones between
-    # replisomes and non-conflicting RNAPs
-    active_chromosome_segments = state["unique"]["chromosomal_segment"][
+    # Check that right number of collisions happened at right coordinates
+    rnap_data = state["listeners"]["rnap_data"]
+    assert rnap_data["n_total_collisions"] == 1
+    assert rnap_data["n_headon_collisions"] == 1
+    assert rnap_data["n_codirectional_collisions"] == 0
+    assert np.array_equal(
+        rnap_data["headon_collision_coordinates"], np.array([-50000], dtype=int)
+    )
+    assert rnap_data["n_empty_fork_collisions"] == 3
+    assert np.array_equal(
+        rnap_data["empty_fork_collision_coordinates"],
+        np.array([-20000, -20000, 20000], dtype=int),
+    )
+    # Check chromosomal segments
+    chromosomal_segments = state["unique"]["chromosomal_segment"][
         state["unique"]["chromosomal_segment"]["_entryState"].view(np.bool_)
     ]
-    assert len(active_chromosome_segments) == 4
-    assert np.all(
-        active_chromosome_segments["boundary_coordinates"]
-        == np.array([[-2000, -1500], [-1500, -1000], [1000, 1500], [1500, 2000]])
+    assert np.array_equal(
+        chromosomal_segments["boundary_coordinates"],
+        np.array(
+            [
+                # Domain 0
+                [-100000, -65000],
+                [-65000, -50000],
+                [45000, 60000],
+                [60000, 75000],
+                [75000, 100000],
+                # Domain 1
+                [-50000, -40000],
+                [-40000, -26000],
+                [-26000, -20000],
+                [20000, 25000],
+                [25000, 35000],
+                [35000, 45000],
+                # Domain 2
+                [-50000, -30000],
+                [-30000, -10000],
+                [-10000, 20000],
+                [20000, 40000],
+                [40000, 45000],
+                # Domain 3
+                [-20000, -15000],
+                [-15000, 10000],
+                [10000, 15000],
+                [15000, 20000],
+                # Domain 4
+                [-20000, 20000],
+            ],
+            dtype=int,
+        ),
+    )
+    assert np.array_equal(
+        chromosomal_segments["boundary_molecule_indexes"],
+        np.array(
+            [
+                # Domain 0: index 5 is gone due to conflict with replisome,
+                # segments were added flanking terC (-1 placeholder index),
+                # index 1 replisome is gone but still exists as placeholder
+                # for replication fork in our superhelical density calculations
+                [-1, 4],
+                [4, 0],
+                [1, 6],
+                [6, 7],
+                [7, -1],
+                # Domain 1: index 1, 2, and 3 replisomes are removed but still exist
+                # here as placeholders
+                [0, 8],
+                [8, 9],
+                [9, 3],
+                [2, 10],
+                [10, 11],
+                [11, 1],
+                # Domain 2: index 1 replisome was removed but still exists here
+                # as a placeholder
+                [0, 12],
+                [12, 13],
+                [13, 14],
+                [14, 15],
+                [15, 1],
+                # Domain 3: index 2 and 3 replisomes are removed but still exist
+                # here as placeholders, index 16 RNAP was removed due to conflict
+                # with replisome placeholder index 3
+                [3, 17],
+                [17, 18],
+                [18, 19],
+                [19, 2],
+                # Domain 4: index 2 and 3 replisomes were removed but still exist
+                # here as placeholders, index 20 and 21 RNAPs were removed due to
+                # conflicts with replisome placeholders
+                [3, 2],
+            ],
+            dtype=int,
+        ),
+    )
+    assert np.array_equal(
+        chromosomal_segments["domain_index"],
+        np.array(
+            [0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 4], dtype=int
+        ),
     )
-    assert np.all(
-        active_chromosome_segments["boundary_molecule_indexes"]
-        == np.array([[-1, 3], [3, 1], [2, 6], [6, -1]])
+    assert np.array_equal(
+        chromosomal_segments["linking_number"],
+        np.array(
+            [
+                # Domain 0: terC segments have 0 linking number, second segment
+                # combines two original segments due to removed RNAP index 5
+                0,
+                2,
+                1,
+                1,
+                0,
+                # Domain 1: No molecule boundaries were changed
+                1,
+                1,
+                1,
+                1,
+                1,
+                1,
+                # Domain 2: No molecule boundaries were changed
+                1,
+                1,
+                1,
+                1,
+                1,
+                # Domain 3: First segment combines two original segments due to
+                # removed RNAP index 16
+                2,
+                1,
+                1,
+                1,
+                # Domain 4: Sole segment combines all three original segments
+                # due to removed RNAP index 20 and 21, leaving only a single
+                # segment between two unoccupied replication forks
+                3,
+            ],
+            dtype=float,
+        ),
     )
 
 
 if __name__ == "__main__":
-    test_superhelical_bug()
+    test_superhelical_removal_sim()
diff --git a/migration/migration_utils.py b/migration/migration_utils.py
index ba8d25e26..ac8be2aaa 100644
--- a/migration/migration_utils.py
+++ b/migration/migration_utils.py
@@ -345,12 +345,17 @@ def run_and_compare(
     if "mRNA_counts" in actual_listeners:
         actual_listeners = {"mrna_counts": actual_listeners}
     # Gene copy number determined by listener after everything updates in wcEcoli
-    # TODO: Move this out of TfBinding process
+    # Empty fork collisions are a new concept in vEcoli
     assert recursive_compare(
         actual_listeners,
         wc_listeners,
         check_keys_strict=False,
-        ignore_keys={"growth", "gene_copy_number"},
+        ignore_keys={
+            "growth",
+            "gene_copy_number",
+            "n_empty_fork_collisions",
+            "empty_fork_collision_coordinates",
+        },
     )
 
 

From 159c0171983128eea51157395ef205d09393534b Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Mon, 16 Dec 2024 22:50:01 -0800
Subject: [PATCH 4/8] Upgrade all packages

---
 uv.lock | 221 ++++++++++++++++++++++++++++----------------------------
 1 file changed, 111 insertions(+), 110 deletions(-)

diff --git a/uv.lock b/uv.lock
index a501589ef..ca9246837 100644
--- a/uv.lock
+++ b/uv.lock
@@ -82,14 +82,14 @@ wheels = [
 
 [[package]]
 name = "aiosignal"
-version = "1.3.1"
+version = "1.3.2"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "frozenlist" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/ae/67/0952ed97a9793b4958e5736f6d2b346b414a2cd63e82d05940032f45b32f/aiosignal-1.3.1.tar.gz", hash = "sha256:54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc", size = 19422 }
+sdist = { url = "https://files.pythonhosted.org/packages/ba/b5/6d55e80f6d8a08ce22b982eafa278d823b541c925f11ee774b0b9c43473d/aiosignal-1.3.2.tar.gz", hash = "sha256:a8c255c66fafb1e499c9351d0bf32ff2d8a0321595ebac3b93713656d2436f54", size = 19424 }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/76/ac/a7305707cb852b7e16ff80eaf5692309bde30e2b1100a1fcacdc8f731d97/aiosignal-1.3.1-py3-none-any.whl", hash = "sha256:f8376fb07dd1e86a584e4fcdec80b36b7f81aac666ebc724e2c090300dd83b17", size = 7617 },
+    { url = "https://files.pythonhosted.org/packages/ec/6a/bc7e17a3e87a2985d3e8f4da4cd0f481060eb78fb08596c42be62c90a4d9/aiosignal-1.3.2-py2.py3-none-any.whl", hash = "sha256:45cde58e409a301715980c2b01d0c28bdde3770d8290b5eb2173759d9acb31a5", size = 7597 },
 ]
 
 [[package]]
@@ -110,7 +110,7 @@ dependencies = [
     { name = "jsonschema" },
     { name = "narwhals" },
     { name = "packaging" },
-    { name = "typing-extensions", marker = "python_full_version == '3.12.8'" },
+    { name = "typing-extensions" },
 ]
 sdist = { url = "https://files.pythonhosted.org/packages/16/b1/f2969c7bdb8ad8bbdda031687defdce2c19afba2aa2c8e1d2a17f78376d8/altair-5.5.0.tar.gz", hash = "sha256:d960ebe6178c56de3855a68c47b516be38640b73fb3b5111c2a9ca90546dd73d", size = 705305 }
 wheels = [
@@ -124,7 +124,7 @@ source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "idna" },
     { name = "sniffio" },
-    { name = "typing-extensions", marker = "python_full_version == '3.12.8'" },
+    { name = "typing-extensions" },
 ]
 sdist = { url = "https://files.pythonhosted.org/packages/f6/40/318e58f669b1a9e00f5c4453910682e2d9dd594334539c7b7817dabb765f/anyio-4.7.0.tar.gz", hash = "sha256:2f834749c602966b7d456a7567cafcb309f96482b5081d14ac93ccd457f9dd48", size = 177076 }
 wheels = [
@@ -206,11 +206,11 @@ wheels = [
 
 [[package]]
 name = "attrs"
-version = "24.2.0"
+version = "24.3.0"
 source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/fc/0f/aafca9af9315aee06a89ffde799a10a582fe8de76c563ee80bbcdc08b3fb/attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346", size = 792678 }
+sdist = { url = "https://files.pythonhosted.org/packages/48/c8/6260f8ccc11f0917360fc0da435c5c9c7504e3db174d5a12a1494887b045/attrs-24.3.0.tar.gz", hash = "sha256:8f5c07333d543103541ba7be0e2ce16eeee8130cb0b3f9238ab904ce1e85baff", size = 805984 }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/6a/21/5b6702a7f963e95456c0de2d495f67bf5fd62840ac655dc451586d23d39a/attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2", size = 63001 },
+    { url = "https://files.pythonhosted.org/packages/89/aa/ab0f7891a01eeb2d2e338ae8fecbe57fcebea1a24dbb64d45801bfab481d/attrs-24.3.0-py3-none-any.whl", hash = "sha256:ac96cd038792094f438ad1f6ff80837353805ac950cd2aa0e0625ef19850c308", size = 63397 },
 ]
 
 [[package]]
@@ -286,11 +286,11 @@ wheels = [
 
 [[package]]
 name = "certifi"
-version = "2024.8.30"
+version = "2024.12.14"
 source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/b0/ee/9b19140fe824b367c04c5e1b369942dd754c4c5462d5674002f75c4dedc1/certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9", size = 168507 }
+sdist = { url = "https://files.pythonhosted.org/packages/0f/bd/1d41ee578ce09523c81a15426705dd20969f5abf006d1afe8aeff0dd776a/certifi-2024.12.14.tar.gz", hash = "sha256:b650d30f370c2b724812bee08008be0c4163b163ddaec3f2546c1caf65f191db", size = 166010 }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/12/90/3c9ff0512038035f59d279fddeb79f5f1eccd8859f06d6163c58798b9487/certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8", size = 167321 },
+    { url = "https://files.pythonhosted.org/packages/a5/32/8f6669fc4798494966bf446c8c4a162e0b5d893dff088afddf76414f70e1/certifi-2024.12.14-py3-none-any.whl", hash = "sha256:1275f7a45be9464efc1173084eaa30f866fe2e47d389406136d332ed4967ec56", size = 164927 },
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 [[package]]
@@ -502,15 +502,15 @@ wheels = [
 
 [[package]]
 name = "debugpy"
-version = "1.8.9"
+version = "1.8.11"
 source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/88/92/15b454c516c4c53cc8c03967e4be12b65a1ea36db3bb4513a7453f75c8d8/debugpy-1.8.9.zip", hash = "sha256:1339e14c7d980407248f09824d1b25ff5c5616651689f1e0f0e51bdead3ea13e", size = 4921695 }
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-    { url = "https://files.pythonhosted.org/packages/50/0a/435d5d7ec64d1c8b422ac9ebe42d2f3b2ac0b3f8a56f5c04dd0f3b7ba83c/tifffile-2024.9.20-py3-none-any.whl", hash = "sha256:c54dc85bc1065d972cb8a6ffb3181389d597876aa80177933459733e4ed243dd", size = 228191 },
+    { url = "https://files.pythonhosted.org/packages/d8/1e/76cbc758f6865a9da18001ac70d1a4154603b71e233f704401fc7d62493e/tifffile-2024.12.12-py3-none-any.whl", hash = "sha256:6ff0f196a46a75c8c0661c70995e06ea4d08a81fe343193e69f1673f4807d508", size = 227538 },
 ]
 
 [[package]]

From 5074a9640e47bb3b464229acabc0a63ae07ea90a Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Mon, 16 Dec 2024 23:40:05 -0800
Subject: [PATCH 5/8] Cleanup and document new function

---
 ecoli/processes/chromosome_structure.py | 34 ++++++++++++++++++++-----
 1 file changed, 27 insertions(+), 7 deletions(-)

diff --git a/ecoli/processes/chromosome_structure.py b/ecoli/processes/chromosome_structure.py
index 217371f88..3f8439e2b 100644
--- a/ecoli/processes/chromosome_structure.py
+++ b/ecoli/processes/chromosome_structure.py
@@ -99,7 +99,6 @@ class ChromosomeStructure(Step):
         "mature_rna_end_positions": [],
         "mature_rna_nt_counts": [],
         "unprocessed_rna_index_mapping": {},
-        "removed_replisome_index": -2,
         "time_step": 1.0,
     }
 
@@ -120,7 +119,6 @@ def __init__(self, parameters=None):
             "relaxed_DNA_base_pairs_per_turn"
         ]
         self.terC_index = self.parameters["terC_index"]
-        self.removed_replisome_index = self.parameters["removed_replisome_index"]
 
         self.n_mature_rnas = self.parameters["n_mature_rnas"]
         self.mature_rna_ids = self.parameters["mature_rna_ids"]
@@ -1243,11 +1241,33 @@ def _compute_new_segment_attributes(
 
 
 def get_last_known_replisome_data(
-    boundary_coordinates,
-    boundary_molecule_indexes,
-    replisome_coordinates,
-    replisome_molecule_indexes,
-):
+    boundary_coordinates: np.ndarray,
+    boundary_molecule_indexes: np.ndarray,
+    replisome_coordinates: np.ndarray,
+    replisome_molecule_indexes: np.ndarray,
+) -> tuple[np.ndarray, np.ndarray]:
+    """
+    Gets the last known coordinates and molecule indexes of both replisomes
+    for a chromosome domain.
+
+    Args:
+        boundary_coordinates: (N, 2) array of chromosomal coordinates of
+            all boundary molecules in the domain during the last time step.
+        boundary_molecule_indexes: (N, 2) array of unique indexes of all
+            boundary molecules in the domain during the last time step.
+        replisome_coordinates: (1,) or (0,) array of chromosomal coordinates of
+            the replisomes in the domain in the current time step.
+        replisome_molecule_indexes: (1,) or (0,) array of unique indexes of the
+            replisomes in the domain in the current time step.
+
+    Returns:
+        Tuple of the following format::
+
+            (
+                (2,) array of last known replisome coordinates in domain,
+                (2,) array of last known replisome molecule indexes in domain
+            )
+    """
     # Sort old boundary coordinates and molecule indexes to find first index
     # where left boundary is non-negative
     boundary_coordinates_argsort = np.argsort(boundary_coordinates[:, 0])

From 340f97e931cef105f96c7864aff64c082aa75ebf Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Tue, 17 Dec 2024 01:00:03 -0800
Subject: [PATCH 6/8] Ensure uniqueness of unique_indices field

---
 ecoli/library/initial_conditions.py     |  5 +----
 ecoli/library/schema.py                 | 12 ++++++++++++
 ecoli/processes/chromosome_structure.py |  4 ++++
 3 files changed, 17 insertions(+), 4 deletions(-)

diff --git a/ecoli/library/initial_conditions.py b/ecoli/library/initial_conditions.py
index 4c94c61dc..6608db23c 100644
--- a/ecoli/library/initial_conditions.py
+++ b/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"])
     )
diff --git a/ecoli/library/schema.py b/ecoli/library/schema.py
index 0a3a7ecfc..9b6cbd1f3 100644
--- a/ecoli/library/schema.py
+++ b/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
 
diff --git a/ecoli/processes/chromosome_structure.py b/ecoli/processes/chromosome_structure.py
index 3f8439e2b..fa56bcc34 100644
--- a/ecoli/processes/chromosome_structure.py
+++ b/ecoli/processes/chromosome_structure.py
@@ -1391,6 +1391,7 @@ def generate_flow(self, config):
     full_chromosomes.flags.writeable = True
     full_chromosomes["_entryState"][0] = 1
     full_chromosomes["domain_index"][0] = 0
+    full_chromosomes["unique_index"][0] = 0
     full_chromosomes.flags.writeable = False
     # Set up chromosome domains
     chromosome_domains, replisome_idx = get_free_indices(
@@ -1399,6 +1400,7 @@ def generate_flow(self, config):
     chromosome_domains.flags.writeable = True
     chromosome_domains["_entryState"][replisome_idx] = 1
     chromosome_domains["domain_index"][replisome_idx] = np.arange(5)
+    chromosome_domains["unique_index"][replisome_idx] = np.arange(5)
     chromosome_domains["child_domains"][replisome_idx] = [
         [1, 2],
         [3, 4],
@@ -1413,6 +1415,7 @@ def generate_flow(self, config):
     oriCs.flags.writeable = True
     oriCs["_entryState"][oriC_idx] = 1
     oriCs["domain_index"][oriC_idx] = [2, 3, 4]
+    oriCs["unique_index"][oriC_idx] = np.arange(3)
     oriCs.flags.writeable = False
     template_initial_state["unique"]["oriC"] = oriCs
     # Set up replisome for actively replicating domain
@@ -1538,6 +1541,7 @@ def generate_flow(self, config):
     )
     chromosomal_segments["domain_index"][segment_idx] = domain_index
     chromosomal_segments["linking_number"][segment_idx] = linking_number
+    chromosomal_segments["unique_index"][segment_idx] = np.arange(len(linking_number))
     chromosomal_segments.flags.writeable = False
     template_initial_state["unique"]["chromosomal_segment"] = chromosomal_segments
     # Since unique numpy updater is an class method, internal

From 04ba75d0ca21f719714d832a4f72ca47a7104997 Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Tue, 17 Dec 2024 03:02:10 -0800
Subject: [PATCH 7/8] Document unique molecule MetadataArray

---
 doc/stores.rst | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/doc/stores.rst b/doc/stores.rst
index b9f8e2dd1..899127af1 100644
--- a/doc/stores.rst
+++ b/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`.

From 2c56c09b1f9c9fa499375785f62929b765e9d76a Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Tue, 17 Dec 2024 03:08:28 -0800
Subject: [PATCH 8/8] Add pre-commit

---
 .pre-commit-config.yaml | 12 ++++++
 README.md               | 13 ++++++
 pyproject.toml          |  3 +-
 uv.lock                 | 93 +++++++++++++++++++++++++++++++++++++----
 4 files changed, 112 insertions(+), 9 deletions(-)
 create mode 100644 .pre-commit-config.yaml

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 000000000..9a4ed56d0
--- /dev/null
+++ b/.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 ]
diff --git a/README.md b/README.md
index 21f5a06f7..b02c3ab11 100644
--- a/README.md
+++ b/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:
diff --git a/pyproject.toml b/pyproject.toml
index e67ad7b10..2d48bf796 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -61,7 +61,8 @@ dev = [
     "pytest",
     "pytest-cov",
     "mypy",
-    "ruff"
+    "ruff",
+    "pre-commit",
 ]
 docs = [
     "Sphinx",
diff --git a/uv.lock b/uv.lock
index ca9246837..61f3ff1a5 100644
--- a/uv.lock
+++ b/uv.lock
@@ -3,7 +3,7 @@ requires-python = "==3.12.8"
 resolution-markers = [
     "platform_system == 'Darwin'",
     "platform_machine == 'aarch64' and platform_system == 'Linux'",
-    "(platform_machine != 'aarch64' and platform_system != 'Darwin') or (platform_system != 'Darwin' and platform_system != 'Linux')",
+    "(platform_machine != 'aarch64' and platform_system == 'Linux') or (platform_system != 'Darwin' and platform_system != 'Linux')",
 ]
 
 [[package]]
@@ -315,6 +315,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/50/b9/db34c4755a7bd1cb2d1603ac3863f22bcecbd1ba29e5ee841a4bc510b294/cffi-1.17.1-cp312-cp312-win_amd64.whl", hash = "sha256:51392eae71afec0d0c8fb1a53b204dbb3bcabcb3c9b807eedf3e1e6ccf2de903", size = 181976 },
 ]
 
+[[package]]
+name = "cfgv"
+version = "3.4.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/11/74/539e56497d9bd1d484fd863dd69cbbfa653cd2aa27abfe35653494d85e94/cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560", size = 7114 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/c5/55/51844dd50c4fc7a33b653bfaba4c2456f06955289ca770a5dbd5fd267374/cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9", size = 7249 },
+]
+
 [[package]]
 name = "charset-normalizer"
 version = "3.4.0"
@@ -552,6 +561,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/46/d1/e73b6ad76f0b1fb7f23c35c6d95dbc506a9c8804f43dda8cb5b0fa6331fd/dill-0.3.9-py3-none-any.whl", hash = "sha256:468dff3b89520b474c0397703366b7b95eebe6303f108adf9b19da1f702be87a", size = 119418 },
 ]
 
+[[package]]
+name = "distlib"
+version = "0.3.9"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/0d/dd/1bec4c5ddb504ca60fc29472f3d27e8d4da1257a854e1d96742f15c1d02d/distlib-0.3.9.tar.gz", hash = "sha256:a60f20dea646b8a33f3e7772f74dc0b2d0772d2837ee1342a00645c81edf9403", size = 613923 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/91/a1/cf2472db20f7ce4a6be1253a81cfdf85ad9c7885ffbed7047fb72c24cf87/distlib-0.3.9-py2.py3-none-any.whl", hash = "sha256:47f8c22fd27c27e25a65601af709b38e4f0a45ea4fc2e710f65755fa8caaaf87", size = 468973 },
+]
+
 [[package]]
 name = "dnspython"
 version = "2.7.0"
@@ -643,6 +661,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/90/2b/0817a2b257fe88725c25589d89aec060581aabf668707a8d03b2e9e0cb2a/fastjsonschema-2.21.1-py3-none-any.whl", hash = "sha256:c9e5b7e908310918cf494a434eeb31384dd84a98b57a30bcb1f535015b554667", size = 23924 },
 ]
 
+[[package]]
+name = "filelock"
+version = "3.16.1"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/9d/db/3ef5bb276dae18d6ec2124224403d1d67bccdbefc17af4cc8f553e341ab1/filelock-3.16.1.tar.gz", hash = "sha256:c249fbfcd5db47e5e2d6d62198e565475ee65e4831e2561c8e313fa7eb961435", size = 18037 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/b9/f8/feced7779d755758a52d1f6635d990b8d98dc0a29fa568bbe0625f18fdf3/filelock-3.16.1-py3-none-any.whl", hash = "sha256:2082e5703d51fbf98ea75855d9d5527e33d8ff23099bec374a134febee6946b0", size = 16163 },
+]
+
 [[package]]
 name = "fiona"
 version = "1.10.1"
@@ -943,6 +970,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/2a/39/e50c7c3a983047577ee07d2a9e53faf5a69493943ec3f6a384bdc792deb2/httpx-0.28.1-py3-none-any.whl", hash = "sha256:d909fcccc110f8c7faf814ca82a9a4d816bc5a6dbfea25d6591d6985b8ba59ad", size = 73517 },
 ]
 
+[[package]]
+name = "identify"
+version = "2.6.3"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/1a/5f/05f0d167be94585d502b4adf8c7af31f1dc0b1c7e14f9938a88fdbbcf4a7/identify-2.6.3.tar.gz", hash = "sha256:62f5dae9b5fef52c84cc188514e9ea4f3f636b1d8799ab5ebc475471f9e47a02", size = 99179 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/c9/f5/09644a3ad803fae9eca8efa17e1f2aef380c7f0b02f7ec4e8d446e51d64a/identify-2.6.3-py2.py3-none-any.whl", hash = "sha256:9edba65473324c2ea9684b1f944fe3191db3345e50b6d04571d10ed164f8d7bd", size = 99049 },
+]
+
 [[package]]
 name = "idna"
 version = "3.10"
@@ -1048,7 +1084,7 @@ name = "ipython"
 version = "8.30.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
-    { name = "colorama", marker = "sys_platform == 'win32'" },
+    { name = "colorama", marker = "(platform_machine != 'aarch64' and platform_system == 'Linux' and sys_platform == 'win32') or (platform_system != 'Darwin' and platform_system != 'Linux' and sys_platform == 'win32')" },
     { name = "decorator" },
     { name = "jedi" },
     { name = "matplotlib-inline" },
@@ -1256,7 +1292,7 @@ version = "5.7.2"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "platformdirs" },
-    { name = "pywin32", marker = "platform_python_implementation != 'PyPy' and sys_platform == 'win32'" },
+    { name = "pywin32", marker = "(platform_machine != 'aarch64' and platform_python_implementation != 'PyPy' and platform_system == 'Linux' and sys_platform == 'win32') or (platform_python_implementation != 'PyPy' and platform_system != 'Darwin' and platform_system != 'Linux' and sys_platform == 'win32')" },
     { name = "traitlets" },
 ]
 sdist = { url = "https://files.pythonhosted.org/packages/00/11/b56381fa6c3f4cc5d2cf54a7dbf98ad9aa0b339ef7a601d6053538b079a7/jupyter_core-5.7.2.tar.gz", hash = "sha256:aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9", size = 87629 }
@@ -1311,7 +1347,7 @@ dependencies = [
     { name = "overrides" },
     { name = "packaging" },
     { name = "prometheus-client" },
-    { name = "pywinpty", marker = "os_name == 'nt'" },
+    { name = "pywinpty", marker = "(os_name == 'nt' and platform_machine != 'aarch64' and platform_system == 'Linux') or (os_name == 'nt' and platform_system != 'Darwin' and platform_system != 'Linux')" },
     { name = "pyzmq" },
     { name = "send2trash" },
     { name = "terminado" },
@@ -1329,7 +1365,7 @@ name = "jupyter-server-terminals"
 version = "0.5.3"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
-    { name = "pywinpty", marker = "os_name == 'nt'" },
+    { name = "pywinpty", marker = "(os_name == 'nt' and platform_machine != 'aarch64' and platform_system == 'Linux') or (os_name == 'nt' and platform_system != 'Darwin' and platform_system != 'Linux')" },
     { name = "terminado" },
 ]
 sdist = { url = "https://files.pythonhosted.org/packages/fc/d5/562469734f476159e99a55426d697cbf8e7eb5efe89fb0e0b4f83a3d3459/jupyter_server_terminals-0.5.3.tar.gz", hash = "sha256:5ae0295167220e9ace0edcfdb212afd2b01ee8d179fe6f23c899590e9b8a5269", size = 31430 }
@@ -1772,6 +1808,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/b9/54/dd730b32ea14ea797530a4479b2ed46a6fb250f682a9cfb997e968bf0261/networkx-3.4.2-py3-none-any.whl", hash = "sha256:df5d4365b724cf81b8c6a7312509d0c22386097011ad1abe274afd5e9d3bbc5f", size = 1723263 },
 ]
 
+[[package]]
+name = "nodeenv"
+version = "1.9.1"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/43/16/fc88b08840de0e0a72a2f9d8c6bae36be573e475a6326ae854bcc549fc45/nodeenv-1.9.1.tar.gz", hash = "sha256:6ec12890a2dab7946721edbfbcd91f3319c6ccc9aec47be7c7e6b7011ee6645f", size = 47437 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/d2/1d/1b658dbd2b9fa9c4c9f32accbfc0205d532c8c6194dc0f2a4c0428e7128a/nodeenv-1.9.1-py2.py3-none-any.whl", hash = "sha256:ba11c9782d29c27c70ffbdda2d7415098754709be8a7056d79a737cd901155c9", size = 22314 },
+]
+
 [[package]]
 name = "notebook"
 version = "7.3.1"
@@ -2083,6 +2128,22 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/4b/59/cf2e88bebdffb7efb7e4f65f4ec9e293040c313d37e3628db87e4f64dca4/polars-1.17.1-cp39-abi3-win_amd64.whl", hash = "sha256:d38156c8259554cbcb17874d91e6dfa9c404335f08a3307496aadfdee46baa31", size = 35931768 },
 ]
 
+[[package]]
+name = "pre-commit"
+version = "4.0.1"
+source = { registry = "https://pypi.org/simple" }
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+    { name = "cfgv" },
+    { name = "identify" },
+    { name = "nodeenv" },
+    { name = "pyyaml" },
+    { name = "virtualenv" },
+]
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+wheels = [
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+]
+
 [[package]]
 name = "prometheus-client"
 version = "0.21.1"
@@ -2418,7 +2479,7 @@ name = "pytest"
 version = "8.3.4"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
-    { name = "colorama", marker = "sys_platform == 'win32'" },
+    { name = "colorama", marker = "(platform_machine != 'aarch64' and platform_system == 'Linux' and sys_platform == 'win32') or (platform_system != 'Darwin' and platform_system != 'Linux' and sys_platform == 'win32')" },
     { name = "iniconfig" },
     { name = "packaging" },
     { name = "pluggy" },
@@ -2991,7 +3052,7 @@ source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "alabaster" },
     { name = "babel" },
-    { name = "colorama", marker = "sys_platform == 'win32'" },
+    { name = "colorama", marker = "(platform_machine != 'aarch64' and platform_system == 'Linux' and sys_platform == 'win32') or (platform_system != 'Darwin' and platform_system != 'Linux' and sys_platform == 'win32')" },
     { name = "docutils" },
     { name = "imagesize" },
     { name = "jinja2" },
@@ -3263,7 +3324,7 @@ version = "0.18.1"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "ptyprocess", marker = "os_name != 'nt'" },
-    { name = "pywinpty", marker = "os_name == 'nt'" },
+    { name = "pywinpty", marker = "(os_name == 'nt' and platform_machine != 'aarch64' and platform_system == 'Linux') or (os_name == 'nt' and platform_system != 'Darwin' and platform_system != 'Linux')" },
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@@ -3465,6 +3526,7 @@ dependencies = [
 [package.optional-dependencies]
 dev = [
     { name = "mypy" },
+    { name = "pre-commit" },
     { name = "pytest" },
     { name = "pytest-cov" },
     { name = "ruff" },
@@ -3503,6 +3565,7 @@ requires-dist = [
     { name = "ortools", specifier = "<=9.9.3963" },
     { name = "pandas" },
     { name = "polars" },
+    { name = "pre-commit", marker = "extra == 'dev'" },
     { name = "pyarrow" },
     { name = "pymunk" },
     { name = "pyqt5" },
@@ -3526,6 +3589,20 @@ requires-dist = [
     { name = "wheel" },
 ]
 
+[[package]]
+name = "virtualenv"
+version = "20.28.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "distlib" },
+    { name = "filelock" },
+    { name = "platformdirs" },
+]
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+wheels = [
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+]
+
 [[package]]
 name = "vivarium-core"
 version = "1.6.5"