Miscellaneous improvements

Author: thalassemia

.github/workflows/docs_deploy.yml

@@ -16,7 +16,7 @@ jobs:
         uses: astral-sh/setup-uv@v7
         with:
           enable-cache: true
-          version: "0.7.12"
+          version: "0.10.6"
       - name: Install Pandoc
         run: sudo apt-get install pandoc
       - name: Install model

.github/workflows/docs_test.yml

@@ -24,7 +24,7 @@ jobs:
         uses: astral-sh/setup-uv@v7
         with:
           enable-cache: true
-          version: "0.7.12"
+          version: "0.10.6"
       - name: Install Pandoc
         run: sudo apt-get install pandoc
       - name: Install model

.github/workflows/pip_audit.yml

@@ -24,7 +24,7 @@ jobs:
         uses: astral-sh/setup-uv@v7
         with:
           enable-cache: true
-          version: "0.7.12"
+          version: "0.10.6"
 
       - name: Audit dependencies and identify vulnerabilities
         run: |

.github/workflows/pr_tests.yml

@@ -38,7 +38,7 @@ jobs:
       uses: astral-sh/setup-uv@v7
       with:
         enable-cache: true
-        version: "0.7.12"
+        version: "0.10.6"
     - name: Install model
       run: USE_CYTHON=1 uv sync --frozen
     - name: Test ParCa reproducibility
@@ -82,7 +82,7 @@ jobs:
       uses: astral-sh/setup-uv@v7
       with:
         enable-cache: true
-        version: "0.7.12"
+        version: "0.10.6"
     - name: Install model
       run: USE_CYTHON=1 uv sync --frozen
     - name: Install nextflow edge
@@ -97,4 +97,14 @@ jobs:
     - name: Show stderr for failed Nextflow tasks
       if: ${{ failure() }}
       run: |
-        nextflow log -q | tail -n 1 | awk '{print $1}' | xargs -I {} nextflow log {} -f name,stderr -F "status == 'FAILED'"
+        RUN_ID=$(nextflow log -q | tail -n 1 | awk '{print $1}')
+        echo "Checking run: $RUN_ID"
+        nextflow log $RUN_ID -f name,workdir,status -F "status == 'FAILED'" | while IFS=$'\t' read -r name workdir status; do
+          echo "===== Failed task: $name ====="
+          if [ -f "$workdir/.command.err" ]; then
+            cat "$workdir/.command.err"
+          else
+            echo "No .command.err file found"
+          fi
+          echo ""
+        done

.github/workflows/pytest.yml

@@ -26,7 +26,7 @@ jobs:
       uses: astral-sh/setup-uv@v7
       with:
         enable-cache: true
-        version: "0.7.12"
+        version: "0.10.6"
     - name: Install model
       run: USE_CYTHON=1 uv sync --frozen --extra dev
     - name: Cache ParCa simulation data
@@ -55,7 +55,7 @@ jobs:
       uses: astral-sh/setup-uv@v7
       with:
         enable-cache: true
-        version: "0.7.12"
+        version: "0.10.6"
     - name: Install model
       run: USE_CYTHON=1 uv sync --frozen --extra dev
     - name: Mypy
@@ -69,7 +69,7 @@ jobs:
       uses: astral-sh/setup-uv@v7
       with:
         enable-cache: true
-        version: "0.7.12"
+        version: "0.10.6"
     - name: Install model
       run: USE_CYTHON=1 uv sync --frozen --extra dev
     - name: Ruff

.gitignore

@@ -13,6 +13,7 @@ out/
 /out
 .idea/
 *.iml
+api_integration/
 
 # User files #
 ################
@@ -67,3 +68,5 @@ trace-*
 #################
 test_sherlock/
 
+# SMS API #
+.hpc_env

.hpc_env_template

@@ -0,0 +1,13 @@
+SLURM_SUBMIT_HOST=
+SLURM_SUBMIT_USER=
+SLURM_SUBMIT_KEY_PATH=
+SLURM_PARTITION=
+SLURM_NODE_LIST=
+SLURM_LOG_BASE_PATH=
+SLURM_QOS=
+SLURM_BASE_PATH=
+
+# Use single thread for BLAS for better performance and reproducibility
+OMP_NUM_THREADS=1
+OPENBLAS_NUM_THREADS=1
+VECLIB_MAXIMUM_THREADS=1

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.11.2
+  rev: v0.15.4
   hooks:
     # Run the linter.
     - id: ruff

README.md

@@ -31,6 +31,7 @@ model parameters (e.g. transcription probabilities). These parameters are used t
 > [Windows Subsystem for Linux](https://learn.microsoft.com/en-us/windows/wsl/install). Refer to the following pages for non-local setups:
 > [Sherlock](https://covertlab.github.io/vEcoli/hpc.html#sherlock),
 > [other HPC cluster](https://covertlab.github.io/vEcoli/hpc.html#other-clusters),
+> [AWS](https://covertlab.github.io/vEcoli/aws.html),
 > [Google Cloud](https://covertlab.github.io/vEcoli/gcloud.html).
 
 ### Prerequisites

configs/default.json

@@ -17,6 +17,12 @@
     "mar_regulon": false,
     "amp_lysis": false,
 
+    "SIM_CPUS": 1,
+    "HYPERQUEUE": false,
+    "HQ_CORES": 1,
+    "SIM_MEM": 4,
+    "SIM_TIME": 4,
+
     "initial_state_file": "",
     "initial_state_overrides": [],
     "initial_state": {},
@@ -35,6 +41,8 @@
 
     "parca_options": {
         "cpus": 1,
+        "memory_gb": 8,
+        "slurm_time_hrs": 1,
         "outdir": "out",
         "operons": true,
         "ribosome_fitting": true,
@@ -56,7 +64,9 @@
     },
 
     "analysis_options": {
-        "cpus": 1
+        "cpus": 1,
+        "memory_gb": 4,
+        "slurm_time_hrs": 4
     },
 
     "gcloud": null,