Merge pull request #34 from RobertArbon/fix_nosubmit

fix: nosubmit runs with default cluster config

.gitignore

@@ -69,5 +69,6 @@ Snakemake
 
 #temp test out
 examples/CyclophilinD_data/abfe/
-examples/abfe_out*
+examples/abfe_*out*
+examples/output
 /src/abfe/_version.py

environment_dev.yml

@@ -0,0 +1,34 @@
+name: abfe
+channels:
+  - bioconda
+  - openbiosim
+  - conda-forge
+  - defaults
+dependencies:
+  - python>=3.8
+  - pip
+  - conda-build
+
+  - snakemake=7.8.5
+  - tabulate=0.8.10
+
+  - gromacs>=2022.2
+
+  - matplotlib
+  - numpy=1.22.4
+  - scipy=1.7.3
+  - pandas
+
+  - mdanalysis
+  - parmed
+  - pdbfixer
+  - biosimspace
+  - openff-toolkit
+  - openff-interchange
+  - black
+
+  - pip:
+    - alchemlyb==2.0.0
+    - pymbar==4.0.1
+    - MDRestraintsGenerator
+

src/abfe_cli/ABFECalculator.py

@@ -36,20 +36,25 @@ def main():
 
     sdf_paths = glob.glob(args.ligand_sdf_dir + "/*.sdf")
 
-    if (args.nosubmit):
-        if (args.nogpu):
-            cluster_config = json.load(open(f"{default_slurm_config_path}", "r"))
-            cluster_config["Snakemake_job"]["queue_job_options"]["cpus-per-task"] = int(args.number_of_parallel_receptor_jobs)
-            cluster_config["Sub_job"]["queue_job_options"]["cpus-per-task"] = int(args.number_of_cpus_per_ligand_job)
-
-        else:
-            cluster_config = json.load(open(f"{default_slurm_config_path}", "r"))
-            cluster_config["Snakemake_job"]["queue_job_options"]["cpus-per-task"] = int(args.number_of_parallel_receptor_jobs)
-            cluster_config["Sub_job"]["queue_job_options"]["cpus-per-task"] = int(args.number_of_parallel_ligand_jobs)
-            cluster_config["Sub_job"]["queue_job_options"]["partition"] = "gpu"
+    if args.nogpu:
+        cluster_config = json.load(open(f"{default_slurm_config_path}", "r"))
+        cluster_config["Snakemake_job"]["queue_job_options"]["cpus-per-task"] = int(
+            args.number_of_parallel_receptor_jobs
+        )
+        cluster_config["Sub_job"]["queue_job_options"]["cpus-per-task"] = int(
+            args.number_of_cpus_per_ligand_job
+        )
 
     else:
-        cluster_config = None
+        cluster_config = json.load(open(f"{default_slurm_config_path}", "r"))
+        cluster_config["Snakemake_job"]["queue_job_options"]["cpus-per-task"] = int(
+            args.number_of_parallel_receptor_jobs
+        )
+        cluster_config["Sub_job"]["queue_job_options"]["cpus-per-task"] = int(
+            args.number_of_parallel_ligand_jobs
+        )
+        cluster_config["Sub_job"]["queue_job_options"]["partition"] = "gpu"
+
 
     res = calculate_abfe(protein_pdb_path=args.protein_pdb_path, ligand_sdf_paths=sdf_paths, out_root_folder_path=args.output_dir_path,
                          cofactor_sdf_path=args.cofactor_sdf_path, approach_name=args.project_name,

src/abfe_cli/ABFECalculatorGmx.py

@@ -33,19 +33,24 @@ def main():
 
     args = parser.parse_args()
 
-    if args.nosubmit:
-        cluster_config = None
+    if args.nogpu:
+        cluster_config = json.load(open(f"{default_slurm_config_path}", "r"))
+        cluster_config["Snakemake_job"]["queue_job_options"]["cpus-per-task"] = int(
+            args.number_of_parallel_receptor_jobs
+        )
+        cluster_config["Sub_job"]["queue_job_options"]["cpus-per-task"] = int(
+            args.number_of_parallel_ligand_jobs
+        )
+
     else:
-        if args.nogpu:
-            cluster_config = json.load(open(f"{default_slurm_config_path}", "r"))
-            cluster_config["Snakemake_job"]["queue_job_options"]["cpus-per-task"] = int(args.number_of_parallel_receptor_jobs)
-            cluster_config["Sub_job"]["queue_job_options"]["cpus-per-task"] = int(args.number_of_parallel_ligand_jobs)
-
-        else:
-            cluster_config = json.load(open(f"{default_slurm_config_path}", "r"))
-            cluster_config["Snakemake_job"]["queue_job_options"]["cpus-per-task"] = int(args.number_of_parallel_receptor_jobs)
-            cluster_config["Sub_job"]["queue_job_options"]["cpus-per-task"] = int(args.number_of_parallel_ligand_jobs)
-            cluster_config["Sub_job"]["queue_job_options"]["partition"] = "gpu"
+        cluster_config = json.load(open(f"{default_slurm_config_path}", "r"))
+        cluster_config["Snakemake_job"]["queue_job_options"]["cpus-per-task"] = int(
+            args.number_of_parallel_receptor_jobs
+        )
+        cluster_config["Sub_job"]["queue_job_options"]["cpus-per-task"] = int(
+            args.number_of_parallel_ligand_jobs
+        )
+        cluster_config["Sub_job"]["queue_job_options"]["partition"] = "gpu"
 
     print(args.gmx_files_root_dir)