Develop

.github/workflows/python-app.yml

@@ -1,21 +1,36 @@
-name: NEAT Unit Tests
+name: NEAT Unit and Integration Tests
 
 on:
+  push:
+    branches: [develop]
   pull_request:
-    branches: [main]
+    branches: [main, develop]
 
 jobs:
-  detailed_test_execution:
+  tests:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: mamba-org/setup-micromamba@v1
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: environment.yml
-          environment-name: test_neat
+          environment-name: neat
           cache-environment: true
 
-      - name: Run unit tests (pytest)
+      - name: Install NEAT (with developer dependencies)
+        shell: bash -l {0}
+        run: |
+          micromamba run -n neat poetry install --with dev
+
+      - name: Run unit tests
+        shell: bash -l {0}
+        run: |
+          micromamba run -n neat pytest -q tests
+
+      - name: Run CLI integration test
+        shell: bash -l {0}
         run: |
-          micromamba run -n test_neat poetry install
-          micromamba run -n test_neat pytest -q tests
+          micromamba run -n neat pytest -q tests/test_cli

CONTRIBUTING.md

@@ -23,6 +23,37 @@ In general, we follow the "fork-and-pull" Git workflow.
 
 Note: Be sure to merge the latest changes before making the pull request. You can increase your chances of a successfull pull request by indicating clearly what branch you are contributing to and making a detailed commit message. It also helps if you open an issue first to let us know you are working on this project.
 
+Running Tests
+-------
+
+We use `pytest` for unit and integration tests.
+
+### Recommended setup
+```bash
+conda env create -f environment.yml
+conda activate neat
+poetry install --with dev
+```
+
+It will also be necessary to gunzip this file:
+
+```bash
+gunzip data/H1N1.fa.gz
+```
+
+To run all tests, use the following command:
+
+```bash
+pytest -q tests
+```
+
+It is also possible to run a subset of tests:
+
+```bash
+pytest -q tests/test_models
+pytest -q tests/test_cli/test_basic_cli.py
+```
+
 License
 -------
 

ChangeLog.md

@@ -1,6 +1,9 @@
 # NEAT has a new home
 NEAT is now a part of the NCSA github and active development will continue here. Please direct issues, comments, and requests to the NCSA issue tracker. Submit pull requests here insead of the old repo.
 
+# NEAT v4.3.5
+- An improvement rather than a bug fix this time. We moved vcf processing into the threaded portion, as our speeds were better than single threaded, but very slow on the vcf writing portion. This sped things up considerably, so we tested and confirmed that it is working as desired and are updating to a new version with improved VCF production in parallel mode.
+
 # NEAT 4.3.4
 - More fixes to bam creation, finalizing parallel code
 

config_template/simple_template.yml

@@ -28,6 +28,6 @@ overwrite_output: .
 
 mode: .
 size: .
-jobs: .
+threads: .
 cleanup_splits: .
 reuse_splits: .

environment.yml

@@ -1,22 +1,12 @@
 name: neat
+
 channels:
-    - conda-forge
-    - bioconda
+  - bioconda
+  - conda-forge
 
 dependencies:
-  - python=3.10.*
-  - biopython=1.85
-  - pkginfo
-  - matplotlib
-  - numpy
-  - pyyaml
+  - python==3.11.*
   - pip
-  - scipy
-  - libgcc=14
-  - htslib
+  - bcftools==1.22*
   - pip:
-    - pysam
-    - frozendict
-    - poetry==1.3.*
-
-  - pytest
+    - poetry==2.2.*

neat/cli/commands/gen_mut_model.py

@@ -90,4 +90,4 @@ def execute(self, arguments: argparse.Namespace):
         """
         compute_mut_runner(arguments.reference, arguments.mutations, arguments.bed, arguments.outcounts,
                            arguments.show_trinuc, arguments.save_trinuc, arguments.human_sample,
-                           arguments.skip_common, arguments.output, arguments.overwrite)
+                           arguments.skip_common, arguments.output_dir, arguments.prefix, arguments.overwrite)

neat/cli/commands/model_fragment_lengths.py

@@ -53,4 +53,4 @@ def execute(self, arguments: argparse.Namespace):
 
         :param arguments: The namespace with arguments and their values.
         """
-        compute_fraglen_runner(arguments.input_file, arguments.min_reads, arguments.output, arguments.overwrite)
+        compute_fraglen_runner(arguments.input_file, arguments.min_reads, arguments.output_dir, arguments.prefix, arguments.overwrite)

neat/cli/commands/model_sequencing_error.py

@@ -95,5 +95,6 @@ def execute(self, arguments: argparse.Namespace):
             # arguments.pileup,
             # arguments.plot,
             arguments.overwrite,
-            arguments.output
+            arguments.output_dir,
+            arguments.prefix
         )