MNT bump to 1.0.2

MANIFEST.in

@@ -1,2 +1,4 @@
 include README.md
-recursive-include scripts *
+include src/ribotools/scripts/get-sample-table
+include src/ribotools/scripts/run-tea
+include src/ribotools/scripts/run-dea

pyproject.toml

@@ -45,15 +45,18 @@ alignment-workflow = "ribotools.htseq_wf.alignment_workflow:main"
 get-ribo-periodic = "ribotools.htseq_wf.get_ribo_periodic:main"
 keep-ribo-periodic = "ribotools.htseq_wf.keep_ribo_periodic:main"
 call-htseq-count = "ribotools.htseq_wf.call_htseq_count:main"
+# DEA/TEA
+get-sample-table = "ribotools.scripts.__main__:get_sample_table"
+run-tea = "ribotools.scripts.__main__:run_tea"
+run-dea = "ribotools.scripts.__main__:run_dea"
 
-# TEA
-[tool.setuptools]
-script-files = [
-  "scripts/get-sample-table",
-  "scripts/run-tea",
-  "scripts/run-dea"
-]
-
+# discouraged - not portable to bioconda
+# [tool.setuptools]
+# script-files = [
+#   "scripts/get-sample-table",
+#   "scripts/run-tea",
+#   "scripts/run-dea"
+# ]
 [project.urls]
 Github = "https://github.com/eboileau/ribotools/"
 Issues = "https://github.com/eboileau/ribotools/issues"

src/ribotools/__init__.py

@@ -1,2 +1,2 @@
-__version_info__ = ("1", "0", "1")
+__version_info__ = ("1", "0", "2")
 __version__ = ".".join(__version_info__)

src/ribotools/scripts/__main__.py

@@ -0,0 +1,29 @@
+import shlex
+import subprocess
+import sys
+from importlib.resources import files
+
+
+def get_sample_table():
+    _run("get-sample-table")
+
+
+def run_dea():
+    _run("run-dea")
+
+
+def run_tea():
+    _run("run-tea")
+
+
+def _get_resource(script):
+    package = "ribotools"
+    resource = "scripts"
+    return files(package).joinpath(resource).joinpath(script)
+
+
+def _run(script):
+    executable = _get_resource(script)
+    cmd = f"{executable} {' '.join(sys.argv[1:])}"
+    safe = shlex.split(cmd)
+    subprocess.run(safe, check=True, stderr=sys.stderr, stdout=sys.stdout, text=True)

scripts/get-sample-table → src/ribotools/scripts/get-sample-table

@@ -4,8 +4,10 @@
 # 1. <-config CONFIG> Yaml config file (same as used for run-htseq-workflow)
 # 2. [{-ribo,-rna}]   Prepare only table for Ribo-seq or RNA-seq samples - default both
 
-library(yaml)
-library(dplyr)
+print("Loading R libraries...")
+
+suppressMessages(library(yaml))
+suppressMessages(library(dplyr))
 
 # defaults
 base.loc <- "count-tables"

scripts/run-dea → src/ribotools/scripts/run-dea

@@ -9,17 +9,19 @@
 # 6. [-delim TAB/CSV]        Field separator character for read.table - default ""
 # 7. [-batch]                If present, uses "batch" from sample table
 
-library(yaml)
-library(DESeq2)
-library(IHW)
-library(ashr)
-library(apeglm)
+print("Loading R libraries...")
 
-library(dplyr)
-library(tibble)
-library(purrr)
+suppressMessages(library(yaml))
+suppressMessages(library(DESeq2))
+suppressMessages(library(IHW))
+suppressMessages(library(ashr))
+suppressMessages(library(apeglm))
 
-library(openxlsx)
+suppressMessages(library(dplyr))
+suppressMessages(library(tibble))
+suppressMessages(library(purrr))
+
+suppressMessages(library(openxlsx))
 
 # ---------------------------------------------------------
 ## Functions

scripts/run-tea → src/ribotools/scripts/run-tea

@@ -12,17 +12,19 @@
 # 8. [-batch]                If present, uses "batch" from sample table
 # 9. [-filter]               If present, filter features with 0 counts in each assay separately
 
-library(yaml)
-library(DESeq2)
-library(IHW)
-library(ashr)
-library(apeglm)
+print("Loading R libraries...")
 
-library(dplyr)
-library(tibble)
-library(purrr)
+suppressMessages(library(yaml))
+suppressMessages(library(DESeq2))
+suppressMessages(library(IHW))
+suppressMessages(library(ashr))
+suppressMessages(library(apeglm))
 
-library(openxlsx)
+suppressMessages(library(dplyr))
+suppressMessages(library(tibble))
+suppressMessages(library(purrr))
+
+suppressMessages(library(openxlsx))
 
 # ---------------------------------------------------------
 ## Functions