Add plumbdb package

modules.nf

@@ -12,7 +12,9 @@ process PROCESS_BINDINGDB {
 
     script:
     """
-    python "${params.scripts}/process_bindingdb.py" --input-dir "${params.bindingDB}"
+    plumbline process-bindingdb \
+    	      --input-directory "${params.bindingDB}" \
+	      --output-directory "./"
     """
 }
 process DOWNLOAD_PDB {
@@ -30,7 +32,8 @@ process DOWNLOAD_PDB {
 
     script:
     """
-    python "${params.scripts}/download_pdb.py" --input-json "${input_json}"
+    plumbline download-pdb \
+              --input-file "${input_json}"
     """
 }
 process PREP_CIF {
@@ -51,7 +54,11 @@ process PREP_CIF {
 
     script:
     """
-    python "${params.scripts}/prep_cif.py" --input-json "${input_json}" --input-cif "${input_cif}" --fasta-sequence "${params.fasta}"
+    plumbline prep-cif \
+              --input-json "${input_json}" \
+              --input-cif "${input_cif}" \
+              --fasta-sequence "${params.fasta}" \
+              --output-directory "./"
     """
 }
 process PREP_FOR_DOCKING {
@@ -71,7 +78,10 @@ process PREP_FOR_DOCKING {
 
     script:
     """
-    asap-cli protein-prep --target SARS-CoV-2-Mpro --pdb-file "${prepped_pdb}" --output-dir "./"
+    plumbline prep-protein-for-docking \
+             --target SARS-CoV-2-Mpro \
+             --pdb-file "${prepped_pdb}" \
+             --output-dir "./"
     """
 }
 process ASSESS_PREPPED_PROTEIN {
@@ -88,7 +98,9 @@ process ASSESS_PREPPED_PROTEIN {
 
     script:
     """
-    python "${params.scripts}/assess_prepped_protein.py" --input-oedu "${design_unit}"
+    plumbline assess-prepped-protein \
+              --input-file "${design_unit}" \
+              --output-directory "./"
     """
 }
 process GENERATE_CONSTRAINED_LIGAND_POSES {
@@ -105,7 +117,10 @@ process GENERATE_CONSTRAINED_LIGAND_POSES {
 
     script:
     """
-    python "${params.scripts}/generate_constrained_ligand_poses.py" --input-sdf "${params.congenericSeries}" --prepped-schema "${prepped_complex_json_schema}"
+    plumbline generate-constrained-ligand-poses \
+              --input-sdf "${params.congenericSeries}" \
+              --prepped-schema "${prepped_complex_json_schema}" \
+              --output-directory "./"
     """
 
 }
@@ -127,10 +142,10 @@ process MAKE_FEC_INPUTS {
     asap-cli alchemy create fecs-workflow.json
 
     asap-cli alchemy plan \
-    -f fecs-workflow.json \
-    --name ${uuid}_plumb_alchemiscale_network \
-    --receptor "${prepped_complex}" \
-    --ligands "${posed_ligands}" \
+             -f fecs-workflow.json \
+             --name ${uuid}_plumb_alchemiscale_network \
+             --receptor "${prepped_complex}" \
+             --ligands "${posed_ligands}" \
     """
 }
 process VISUALIZE_NETWORK {
@@ -147,6 +162,8 @@ process VISUALIZE_NETWORK {
 
     script:
     """
-    python "${params.scripts}/visualize_network.py" --network-graphml "${network_graph}"
+    plumbline visualize-network \
+              --network-graphml "${network_graph}" \
+              --output-directory "./"
     """
-}
+}

pkg/README.md

@@ -0,0 +1,11 @@
+# plumbdb
+
+## Installation
+
+Since `plumbdb` is not yet registered with conda-forge, follow the developer installation instructions at [docs/developer.md](docs/developer.md#installation).
+
+## Usage
+
+### Command line
+
+`plumbdb` is usable via command line through the `plumbline` CLI application.

pkg/docs/developer.md

@@ -0,0 +1,19 @@
+# Developer documentation
+
+## Installation
+
+`plumbdb` can currently only be installed via its python source with its dependencies handled by `conda`.
+
+```bash
+conda create -n plumbdb_dev -f env.yaml
+conda activate plumbdb_dev
+pip install -e ".[dev]"
+```
+
+## Running tests
+
+Tests are performed with [`pytest`](https://docs.pytest.org/), which is automatically installed as part of the `test` dependency group specified in `pyproject.toml`. With the test environment active and from within `plumb/pkg/`, run:
+
+```bash
+python -m pytest src/
+```

pkg/env.yaml

@@ -0,0 +1,11 @@
+name: plumbdb
+channels:
+  - conda-forge
+  - openeye
+
+dependencies:
+  - python=3.11
+  - openeye-toolkits
+  - asapdiscovery
+  - openfe
+  - click

pkg/pyproject.toml

@@ -0,0 +1,31 @@
+[build-system]
+requires = [
+    "setuptools>=77.0.3",
+    "setuptools-scm>=8",
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "plumbdb"
+description = ""
+readme = "README.md"
+authors = [
+	{name = "Ariana Brenner Clerkin", email = "ariana.clerkin@choderlab.org"}
+]
+license = "MIT"
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "Operating System :: POSIX",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Chemistry",
+]
+requires-python = ">= 3.11"
+dynamic = ["version"]
+
+[project.scripts]
+plumbline = "plumbdb.cli:cli"
+
+[project.optional-dependencies]
+test = ["pytest"]
+dev = ["pytest", "ruff"]