From 00916ff4a2e3c18b6e2b8355dede4fd1d1752073 Mon Sep 17 00:00:00 2001
From: Luke Zoltan Kelley <lzkelley@gmail.com>
Date: Wed, 7 Feb 2024 12:03:23 -0800
Subject: [PATCH] BUG: readthedocs build error, 3

---
 docs/source/conf.py                           |  8 ++++----
 docs/source/index.rst                         |  1 -
 holodeck/extensions.py                        |  2 +-
 .../{_librarian.py => old_librarian_py}       |  0
 setup.py                                      | 19 ++++++++++++++-----
 5 files changed, 19 insertions(+), 11 deletions(-)
 rename holodeck/librarian/{_librarian.py => old_librarian_py} (100%)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index fea993c9..3bd248d5 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -26,7 +26,7 @@
     'sphinx.ext.mathjax',
 ]
 
-templates_path = ['_templates']
+templates_path = []
 exclude_patterns = []
 
 
@@ -41,7 +41,6 @@
 
 # Define the configuration for sphinx-apidoc
 apidoc_module_dir = 'source/apidoc_modules'
-apidoc_output_dir = 'source'
 apidoc_excluded_paths = ['../holodeck/detstats.py', '../holodeck/anisotropy.py', '../holodeck/librarian/_librarian.py']
 apidoc_command_options = ' '.join([
     '-e',  # Create separate files for each module
@@ -54,11 +53,12 @@
 def run_apidoc(_):
     from sphinx.ext.apidoc import main
     argv = [
-        '-o', apidoc_module_dir,
         '-M',
         '-T',
         '-f',
-        '../holodeck'
+        '-o', apidoc_module_dir,
+        '../holodeck',
+        *apidoc_excluded_paths,
     ]
     main(argv)
 
diff --git a/docs/source/index.rst b/docs/source/index.rst
index cbc40140..8f475702 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -2,7 +2,6 @@
 holodeck
 ========
 
-
 |version| |build| |docs|
 
 .. |version|
diff --git a/holodeck/extensions.py b/holodeck/extensions.py
index 5ca15212..7e480972 100644
--- a/holodeck/extensions.py
+++ b/holodeck/extensions.py
@@ -7,7 +7,7 @@
 import holodeck.librarian
 import numpy as np
 import kalepy as kale
-from holodeck.sams import cyutils as sam_cyutils
+from holodeck.sams import sam_cyutils
 
 PSPACE = holo.librarian.param_spaces_classic.PS_Classic_Phenom_Uniform
 
diff --git a/holodeck/librarian/_librarian.py b/holodeck/librarian/old_librarian_py
similarity index 100%
rename from holodeck/librarian/_librarian.py
rename to holodeck/librarian/old_librarian_py
diff --git a/setup.py b/setup.py
index d66fd3ec..a43e1f4c 100644
--- a/setup.py
+++ b/setup.py
@@ -6,32 +6,40 @@
 
 """
 
+from pathlib import Path
 from os.path import abspath, join
 from setuptools import setup, find_packages
 from setuptools.extension import Extension
 from Cython.Build import cythonize
 import numpy as np
 
+SETUP_PATH = Path(__file__).absolute().resolve().parent
+print(f"{SETUP_PATH=}")
+
 # ---- Prepare Meta-Data ----
 
 # NOTE: `short_description` gets first line of `__doc__` only (linebreaks not allowed by setuptools)
 short_description = __doc__.strip().split('\n')[0]
 
-with open("README.md", "r") as handle:
+fname_desc = SETUP_PATH.joinpath("README.md")
+with open(fname_desc, "r") as handle:
     long_description = handle.read()
 
-with open("requirements.txt", "r") as handle:
+fname_reqs = SETUP_PATH.joinpath("requirements.txt")
+with open(fname_reqs, "r") as handle:
     requirements = handle.read()
 
-with open('holodeck/version.txt') as handle:
+fname_vers = SETUP_PATH.joinpath('./holodeck/version.txt')
+with open(fname_vers) as handle:
     version = handle.read().strip()
 
 
 # ---- Handle cython submodules ----
 
+fname_cyutils = SETUP_PATH.joinpath("holodeck", "cyutils.pyx")
 ext_cyutils = Extension(
     "holodeck.cyutils",    # specify the resulting name/location of compiled extension
-    sources=[join('.', 'holodeck', 'cyutils.pyx')],   # location of source code
+    sources=[str(fname_cyutils)],   # location of source code
     # define parameters external libraries
     include_dirs=[
         np.get_include()
@@ -47,9 +55,10 @@
     extra_compile_args=['-Wno-unreachable-code-fallthrough', '-Wno-unused-function'],
 )
 
+fname_sam_cyutils = SETUP_PATH.joinpath("holodeck", "sams", "sam_cyutils.pyx")
 ext_sam_cyutils = Extension(
     "holodeck.sams.sam_cyutils",    # specify the resulting name/location of compiled extension
-    sources=[join('.', 'holodeck', 'sams', 'sam_cyutils.pyx')],   # location of source code
+    sources=[str(fname_sam_cyutils)],   # location of source code
     # define parameters external libraries
     include_dirs=[
         np.get_include()