Merge branch 'master' of github.com:computationalmodelling/fidimag into nebm-kf

Author: davidcortesortuno

.readthedocs.yml

@@ -0,0 +1,13 @@
+version: 2
+
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "mambaforge-22.9"
+
+conda:
+  environment: doc/environment.yml
+
+sphinx:
+  # Path to your Sphinx configuration file.
+  configuration: doc/conf.py

doc/conf.py

@@ -78,7 +78,7 @@
 
 html_theme_options = {
     "github_url": "https://github.com/computationalmodelling/fidimag",
-    "use_edit_page_button": True,
+    # "use_edit_page_button": True,
     "show_toc_level": 1,
     # "navbar_align": "right",  # For testing that the navbar items align properly
 }

pyproject.toml

@@ -3,7 +3,8 @@ name = "fidimag"
 dynamic = ["version"]
 description = "Atomistic and Finite-DIfference microMAGnetic code, based on Python, Cython and C "
 readme = "README.md"
-license-files = "LICENSE.txt"
+# Not fully supported:
+# license-files = ["LICENSE.txt"]
 # license = "BSD-2-Clause"
 requires-python = ">= 3.10"
 dependencies = [

readthedocs.yml

@@ -14,15 +14,16 @@
 sReset = "\x1b[0m"
 
 
-MODULE_DIR = Path(__file__).parent  # This should be the abs path
+ABS_MODULE_DIR = Path(__file__).parent  # This should be the abs path
+MODULE_DIR = Path('.')  # This should be the rel path (setup.py requires rel paths for pip -e)
 print(MODULE_DIR)
-INCLUDE_DIR = MODULE_DIR / 'local/include'
-LIB_DIR = MODULE_DIR / 'local/lib'
-LIB_DIR64 = MODULE_DIR / 'local/lib64'
+INCLUDE_DIR = ABS_MODULE_DIR / 'local/include'
+# Use absolute paths for the sundials/fftw libs:
+LIB_DIR = ABS_MODULE_DIR / 'local/lib'
+LIB_DIR64 = ABS_MODULE_DIR / 'local/lib64'
 
-# Paths are relative to the extensions directory in: fidimag/extensions/
-# So we use "../..". Otherwise, we have to add the LIB folder to LD_LIBRARY_PATH env variable
-com_link = ['-Wl,-rpath,../../{},-rpath,../../{}'.format(str(LIB_DIR), str(LIB_DIR64)), '-fopenmp']
+# rpath: run-time search path for the sundials (cvode) and fftw library objects
+com_link = ['-Wl,-rpath,{},-rpath,{}'.format(str(LIB_DIR), str(LIB_DIR64)), '-fopenmp']
 lib_paths = [str(LIB_DIR), str(LIB_DIR64)]
 com_libs = ['m', 'fftw3_omp', 'fftw3', 'sundials_cvodes', 'sundials_nvecserial', 'sundials_nvecopenmp', 'blas', 'lapack']
 com_args = ['-O3', '-Wno-cpp', '-Wno-unused-function', '-Wall', '-std=c99', '-fopenmp']
@@ -34,7 +35,7 @@
 if 'FFTW_INC' in os.environ:
      com_inc.append(os.environ['FFTW_INC'])
 
-# Find all .pyx files with extensions (source files)
+# Find all .pyx files with extensions (source files) -> relative paths
 ROOT_DIR = MODULE_DIR / 'fidimag'
 source_files = [s for s in ROOT_DIR.rglob('*.pyx')]  # Paths