From b3438a188280d3eb64722bba4bfa0fa0ac444f81 Mon Sep 17 00:00:00 2001
From: Adam Taranto <adam.p.taranto@gmail.com>
Date: Sun, 5 Jan 2025 02:35:39 +1100
Subject: [PATCH] Fix dists (#736)

* Add libmagick of linux note

* include cython modules in wheel

* Style fixes by Black

* include src dir in dist tarball

* format headings

---------

Co-authored-by: Adamtaranto <Adamtaranto@users.noreply.github.com>
---
 README.md       | 22 ++++++++++++++++------
 pyproject.toml  | 18 +++++++++++++-----
 src/jcvi/cli.py | 11 +++++++----
 3 files changed, 36 insertions(+), 15 deletions(-)

diff --git a/README.md b/README.md
index e6767f86..98b8ca61 100644
--- a/README.md
+++ b/README.md
@@ -106,6 +106,15 @@ full-fledged applications.
 
 JCVI requires Python3 between v3.8 and v3.12.
 
+Some graphics modules require the [ImageMagick](https://imagemagick.org/index.php) library. 
+
+On MacOS this can be installed using Conda (see next section). If you are using a linux system (i.e. Ubuntu) you can install ImageMagick using apt-get:
+
+```bash
+sudo apt-get update
+sudo apt-get install libmagickwand-dev
+```
+
 A few modules may ask for locations of external programs,
 if the executable cannot be found in your `PATH`. 
 
@@ -115,11 +124,9 @@ The external programs that are often used are:
 - [BEDTOOLS](http://code.google.com/p/bedtools/)
 - [EMBOSS](http://emboss.sourceforge.net/)
 
-## Installation
-
-**Installing JCVI in a Conda environment:**
+### Managing dependencies with Conda
 
-You can create a Conda environment with Python 3.12 and basic dependencies for JCVI using the YAML files in this repo.
+You can use the the YAML files in this repo to create an environment with basic JCVI dependencies.
 
 If you are new to Conda, we recommend the [Miniforge](https://conda-forge.org/download/) distribution.
 
@@ -142,8 +149,9 @@ conda activate jcvi-osx64
 
 After activating the Conda environment install JCVI using one of the following options.
 
+## Installation
 
-**Installation options:**  
+### Installation options
 
 1) Use pip to install the latest development version directly from this repo.
 
@@ -164,7 +172,7 @@ git clone git://github.com/tanghaibao/jcvi.git && cd jcvi
 pip install -e '.[tests]'
 ```
 
-**Test Installation:**  
+### Test Installation
 
 If installed successfully, you can check the version with:
 
@@ -172,6 +180,8 @@ If installed successfully, you can check the version with:
 jcvi --version
 ```
 
+## Usage 
+
 Use `python -m` to call any of the modules installed with JCVI.
 
 Most of the modules in this package contains multiple actions. To use
diff --git a/pyproject.toml b/pyproject.toml
index a87b262b..aaec128c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,8 +9,6 @@ requires = [
 ]
 build-backend = "hatchling.build"
 
-[tool.hatch.build.hooks.custom]
-path = "build.py"
 
 # Project metadata and configuration
 [project]
@@ -87,14 +85,22 @@ jcvi = "jcvi.cli:main"
 allow-direct-references = true
 
 [tool.hatch.build]
-packages = ["src/jcvi"]
+packages = ["src"]
+artifacts = [
+    "src/jcvi/**/*.so",  # Linux/Mac shared objects
+    "src/jcvi/**/*.pyd", # Windows shared objects
+    "src/jcvi/**/*.c"    # Generated C files
+]
 
-[tool.hatch.version]
-source = "vcs"
+[tool.hatch.build.hooks.custom]
+path = "build.py"
 
 [tool.hatch.build.hooks.vcs]
 version-file = "src/jcvi/_version.py"
 
+[tool.hatch.version]
+source = "vcs"
+
 [tool.hatch.version.vcs]
 tag-pattern = "v*"
 fallback-version = "0.0.0"
@@ -106,5 +112,7 @@ include = [
     "README.md",
 ]
 
+force-include = { "build.py" = "build.py", "setup.py" = "setup.py"}
+
 [tool.hatch.build.targets.wheel]
 packages = ["src/jcvi"]
\ No newline at end of file
diff --git a/src/jcvi/cli.py b/src/jcvi/cli.py
index b55e091a..6af68823 100644
--- a/src/jcvi/cli.py
+++ b/src/jcvi/cli.py
@@ -2,11 +2,14 @@
 import argparse
 from . import __version__
 
+
 def main():
     parser = argparse.ArgumentParser()
-    parser.add_argument('--version', action='version', 
-                       version=f'%(prog)s {__version__}')
+    parser.add_argument(
+        "--version", action="version", version=f"%(prog)s {__version__}"
+    )
     args = parser.parse_args()
 
-if __name__ == '__main__':
-    main()
\ No newline at end of file
+
+if __name__ == "__main__":
+    main()