Enable managing app via setup.py

While the application is developed with GNU Guix, the end user might
not be using it, and therefore, this commit provides a way for the
user to install the application with the usual python package
management systems.

10 files changed, 59 insertions, 3 deletions

diff --git a/.gitignore b/.gitignore
index 7135ef6..91958fd 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,8 @@
 /**/*~
 /**/*.pyc
 /.hypothesis
-/instance
\ No newline at end of file
+/instance
+/build
+/dist
+/bdist
+/*.egg-info
\ No newline at end of file
diff --git a/MANIFEST.in b/MANIFEST.in
new file mode 100644
index 0000000..65f3dd8
--- /dev/null
+++ b/MANIFEST.in
@@ -0,0 +1,3 @@
+include README.org
+include etc/*
+exclude etc/*~
\ No newline at end of file
diff --git a/README.org b/README.org
index 53ac63c..ecf7815 100644
--- a/README.org
+++ b/README.org
@@ -58,6 +58,18 @@ To check for correct type usage in the application, run:
 
 *** Command-Line Version
 
+Clone this repository
+#+BEGIN_SRC shell
+  git clone http://git.genenetwork.org/fredmanglis/gnqc_py.git
+#+END_SRC
+then install the application
+#+BEGIN_SRC shell
+  $ python3 -m venv .venv
+  $ source .venv/bin/activate
+  (.venv) $ pip install .
+#+END_SRC
+
+
 To run qc against a file, the syntax is:
 #+BEGIN_SRC shell
   python3 -m qc [--strainsfile <strainsfile-path>] [--verbose] <filetype> <filepath>
diff --git a/strains.csv b/etc/strains.csv
index 50ab6c1..50ab6c1 100644
--- a/strains.csv
+++ b/etc/strains.csv
diff --git a/mypy.ini b/mypy.ini
new file mode 100644
index 0000000..ba70688
--- /dev/null
+++ b/mypy.ini
@@ -0,0 +1,10 @@
+[mypy]
+
+[mypy-flask.*]
+ignore_missing_imports = True
+
+[mypy-pytest.*]
+ignore_missing_imports = True
+
+[mypy-hypothesis.*]
+ignore_missing_imports = True
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..087fa09
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,3 @@
+[build-system]
+requires=["setuptools"]
+build-backend = "setuptools.build_meta"
\ No newline at end of file
diff --git a/scripts/__init__.py b/scripts/__init__.py
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/scripts/__init__.py
diff --git a/qc.py b/scripts/qc.py
index fee74cb..09758cb 100644
--- a/qc.py
+++ b/scripts/qc.py
@@ -34,7 +34,7 @@ def cli_argument_parser():
             "If an absolute path is not provided, then the file will be relative to"
             f"\t'{os.getcwd()}'"))
     default_strains_file = os.path.join(
-        os.path.dirname(__file__), "strains.csv")
+        os.path.dirname(os.path.dirname(__file__)), "etc/strains.csv")
     parser.add_argument(
         "-s", "--strainsfile",
         help=(
@@ -75,7 +75,7 @@ def main():
         return 1
 
     if not os.path.exists(args.strainsfile):
-        print("The file '{args.strainsfile}' does not exist.", file=sys.stderr)
+        print(f"The file '{args.strainsfile}' does not exist.", file=sys.stderr)
         return 2
 
     if not is_file_mime(args.filepath, "text/tab-separated-values"):
diff --git a/setup.cfg b/setup.cfg
new file mode 100644
index 0000000..72baf7c
--- /dev/null
+++ b/setup.cfg
@@ -0,0 +1,21 @@
+[metadata]
+name = qc
+version = 0.0.1
+author = Frederick M. Muriithi
+description = Quality control app for average and standard-error files
+url = http://git.genenetwork.org/fredmanglis/gnqc_py
+
+[options]
+packages =
+    tests
+    scripts
+    quality_control
+install_requires =
+    rq
+    python-magic
+exclude = tests*
+include_package_data = True
+
+[options.entry_points]
+console_scripts =
+    qc = scripts.qc:main
\ No newline at end of file
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..6068493
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,3 @@
+from setuptools import setup
+
+setup()