rename pyo3_branchwater to sourmash_plugin_branchwater

sourmash-bio · Nov 29, 2023 · 031e799 · 031e799
1 parent cca04be
commit 031e799
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Showing 8 changed files with 80 additions and 73 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -5,7 +5,7 @@ edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 [lib]
-name = "pyo3_branchwater" # CTB: should we change this, too?
+name = "sourmash_plugin_branchwater"
 crate-type = ["cdylib"]
 
 [dependencies]

diff --git a/Makefile b/Makefile
@@ -16,8 +16,8 @@ wheel:
 	$(PYTHON) -m maturin build -r
 
 sdist:
-	rm -f target/wheels/pyo3_branchwater-*.tar.gz
+	rm -f target/wheels/sourmash_plugin_branchwater-*.tar.gz
 	$(PYTHON) -m maturin sdist
 
 upload_sdist: sdist
-	twine upload target/wheels/pyo3_branchwater-*.tar.gz
+	twine upload target/wheels/sourmash_plugin_branchwater-*.tar.gz
diff --git a/README.md b/README.md
@@ -37,7 +37,7 @@ This quickstart demonstrates `multisearch` using
 
 You'll need rust, Python, and maturin to build, and sourmash to run. See [environment.yml](environment.yml) for a list of conda packages, and developer docs below for example command lines.
 
-### 2. Install pyo3_branchwater.
+### 2. Install sourmash_plugin_branchwater.
 
 Install this repo in developer mode:
 ```

diff --git a/pyproject.toml b/pyproject.toml
@@ -30,6 +30,13 @@ index = "sourmash_plugin_branchwater:Branchwater_Index"
 check = "sourmash_plugin_branchwater:Branchwater_Check"
 manysketch = "sourmash_plugin_branchwater:Branchwater_Manysketch"
 
+[project.optional-dependencies]
+test = [
+  "pytest>=6.2.4,<7.5.0",
+  "pytest-cov>=2.12,<5.0",
+  "pytest-xdist",
+  "pandas",
+]
 
 [tool.maturin]
 python-source = "src/python"

diff --git a/src/lib.rs b/src/lib.rs
@@ -1,4 +1,4 @@
-/// Python interface Rust code for pyo3_branchwater.
+/// Python interface Rust code for sourmash_plugin_branchwater.
 use pyo3::prelude::*;
 
 #[macro_use]
@@ -220,7 +220,7 @@ fn do_manysketch(filelist: String, param_str: String, output: String) -> anyhow:
 }
 
 #[pymodule]
-fn pyo3_branchwater(_py: Python, m: &PyModule) -> PyResult<()> {
+fn sourmash_plugin_branchwater(_py: Python, m: &PyModule) -> PyResult<()> {
     m.add_function(wrap_pyfunction!(do_manysearch, m)?)?;
     m.add_function(wrap_pyfunction!(do_fastgather, m)?)?;
     m.add_function(wrap_pyfunction!(do_fastmultigather, m)?)?;

diff --git a/src/python/sourmash_plugin_branchwater/__init__.py b/src/python/sourmash_plugin_branchwater/__init__.py
@@ -8,10 +8,10 @@
 
 from . import pyo3_branchwater
 
-__version__ = importlib.metadata.version("pyo3_branchwater")
+__version__ = importlib.metadata.version("sourmash_plugin_branchwater")
 
 def print_version():
-    notify(f"=> pyo3_branchwater {__version__}; cite Irber et al., doi: 10.1101/2022.11.02.514947\n")
+    notify(f"=> sourmash_plugin_branchwater {__version__}; cite Irber et al., doi: 10.1101/2022.11.02.514947\n")
 
 
 def get_max_cores():
@@ -32,7 +32,7 @@ def set_thread_pool(user_cores):
     num_threads = min(avail_threads, user_cores) if user_cores else avail_threads
     if user_cores and user_cores > avail_threads:
         notify(f"warning: only {avail_threads} threads available, using {avail_threads}")
-    actual_rayon_cores = pyo3_branchwater.set_global_thread_pool(num_threads)
+    actual_rayon_cores = sourmash_plugin_branchwater.set_global_thread_pool(num_threads)
     return actual_rayon_cores
 
 
@@ -68,13 +68,13 @@ def main(self, args):
         notify(f"searching all sketches in '{args.query_paths}' against '{args.against_paths}' using {num_threads} threads")
 
         super().main(args)
-        status = pyo3_branchwater.do_manysearch(args.query_paths,
-                                                args.against_paths,
-                                                args.threshold,
-                                                args.ksize,
-                                                args.scaled,
-                                                args.moltype,
-                                                args.output)
+        status = sourmash_plugin_branchwater.do_manysearch(args.query_paths,
+                                                           args.against_paths,
+                                                           args.threshold,
+                                                           args.ksize,
+                                                           args.scaled,
+                                                           args.moltype,
+                                                           args.output)
         if status == 0:
             notify(f"...manysearch is done! results in '{args.output}'")
         return status
@@ -115,14 +115,14 @@ def main(self, args):
 
         notify(f"gathering all sketches in '{args.query_sig}' against '{args.against_paths}' using {num_threads} threads")
         super().main(args)
-        status = pyo3_branchwater.do_fastgather(args.query_sig,
-                                                args.against_paths,
-                                                int(args.threshold_bp),
-                                                args.ksize,
-                                                args.scaled,
-                                                args.moltype,
-                                                args.output_gather,
-                                                args.output_prefetch)
+        status = sourmash_plugin_branchwater.do_fastgather(args.query_sig,
+                                                           args.against_paths,
+                                                           int(args.threshold_bp),
+                                                           args.ksize,
+                                                           args.scaled,
+                                                           args.moltype,
+                                                           args.output_gather,
+                                                           args.output_prefetch)
         if status == 0:
             notify(f"...fastgather is done! gather results in '{args.output_gather}'")
             if args.output_prefetch:
@@ -161,13 +161,13 @@ def main(self, args):
 
         notify(f"gathering all sketches in '{args.query_paths}' against '{args.against_paths}' using {num_threads} threads")
         super().main(args)
-        status = pyo3_branchwater.do_fastmultigather(args.query_paths,
-                                                     args.against_paths,
-                                                     int(args.threshold_bp),
-                                                     args.ksize,
-                                                     args.scaled,
-                                                     args.moltype,
-                                                     args.output)
+        status = sourmash_plugin_branchwater.do_fastmultigather(args.query_paths,
+                                                                args.against_paths,
+                                                                int(args.threshold_bp),
+                                                                args.ksize,
+                                                                args.scaled,
+                                                                args.moltype,
+                                                                args.output)
         if status == 0:
             notify(f"...fastmultigather is done!")
         return status
@@ -203,13 +203,13 @@ def main(self, args):
         notify(f"indexing all sketches in '{args.siglist}'")
 
         super().main(args)
-        status = pyo3_branchwater.do_index(args.siglist,
-                                                args.ksize,
-                                                args.scaled,
-                                                args.moltype,
-                                                args.output,
-                                                args.save_paths,
-                                                False) # colors - currently must be false?
+        status = sourmash_plugin_branchwater.do_index(args.siglist,
+                                                      args.ksize,
+                                                      args.scaled,
+                                                      args.moltype,
+                                                      args.output,
+                                                      args.save_paths,
+                                                      False) # colors - currently must be false?
         if status == 0:
             notify(f"...index is done! results in '{args.output}'")
         return status
@@ -227,7 +227,7 @@ def __init__(self, p):
     def main(self, args):
         notify(f"checking index '{args.index}'")
         super().main(args)
-        status = pyo3_branchwater.do_check(args.index, args.quick)
+        status = sourmash_plugin_branchwater.do_check(args.index, args.quick)
         if status == 0:
             notify(f"...index is ok!")
         return status
@@ -266,13 +266,13 @@ def main(self, args):
         notify(f"searching all sketches in '{args.query_paths}' against '{args.against_paths}' using {num_threads} threads")
 
         super().main(args)
-        status = pyo3_branchwater.do_multisearch(args.query_paths,
-                                                 args.against_paths,
-                                                 args.threshold,
-                                                 args.ksize,
-                                                 args.scaled,
-                                                 args.moltype,
-                                                 args.output)
+        status = sourmash_plugin_branchwater.do_multisearch(args.query_paths,
+                                                            args.against_paths,
+                                                            args.threshold,
+                                                            args.ksize,
+                                                            args.scaled,
+                                                            args.moltype,
+                                                            args.output)
         if status == 0:
             notify(f"...multisearch is done! results in '{args.output}'")
         return status
@@ -309,9 +309,9 @@ def main(self, args):
         notify(f"sketching all files in '{args.fromfile_csv}' using {num_threads} threads")
 
         super().main(args)
-        status = pyo3_branchwater.do_manysketch(args.fromfile_csv,
-                                            args.param_string,
-                                            args.output)
+        status = sourmash_plugin_branchwater.do_manysketch(args.fromfile_csv,
+                                                           args.param_string,
+                                                           args.output)
         if status == 0:
             notify(f"...manysketch is done! results in '{args.output}'")
         return status
diff --git a/src/utils.rs b/src/utils.rs
@@ -1,4 +1,4 @@
-/// Utility functions for pyo3_branchwater.
+/// Utility functions for sourmash_plugin_branchwater.
 use rayon::prelude::*;
 use sourmash::encodings::HashFunctions;