update docs

docs/Installation/installation.rst

@@ -81,6 +81,9 @@ Downloading and installing S4 (start from the directory in which you want to dow
 Here we download my fork of S4 (modified to be compatible with Python3), move to the downloaded directory, and then we make the Python extension.
 If you activated the virtual environment before running this, S4 should automatically install into that virtual environment.
 
+**Note for users of new Mac devices with Apple M1/ARM chips:** You can install packages using Homebrew as described above,
+but instead of :literal:`make S4_pyext`, you should run :literal:`make S4_pyext --file="Makefile.m1"`.
+
 .. _install:
 
 Installing RayFlare
@@ -128,8 +131,8 @@ things like 'pip install' will point to the right place.
 
 As an alternative to the venv method above, PyCharm also has built-in support for making a new virtualenv environment
 based on one of your 'system interpreters' (these are the versions of Python installed -- if you followed the
-instructions above and are on Ubuntu 18, these are probably Python2.7, Python3.6 and the newly-installed
-Python3.8). You can create one of those environments by going to Project Interpreter in the same way, adding a new
+instructions above and are on Ubuntu 20, these are probably Python2.7, Python3.8 and possibly the newly-installed
+Python3.10). You can create one of those environments by going to Project Interpreter in the same way, adding a new
 environment and selecting 'Virtualenv environment' with the relevant base interpreter.
 
 Installing S4 on Windows

docs/Installation/python_install.rst

@@ -1,6 +1,9 @@
-========================================
-Python versions and installing Python3.8
-========================================
+==========================================
+Python versions and installing Python3.10
+==========================================
+
+Ubuntu
+-------
 
 On Ubuntu, Python is an integral part of the operating system, so there will already be a version
 (likely more than one version, usually a version of Python2 and a version of Python3) installed
@@ -10,39 +13,50 @@ working in a virtual environment. This also avoids having to use 'sudo' to insta
 There are various packages for creating virtual environments, all with confusingly similar names -- I use
 venv (not to be confused with virtualenv or pipenv...).
 
-Currently, Ubuntu18 does not come with Python3.8 (the latest stable Python version), by default, but you can
-install it pretty easily. From a terminal window (command line):
+On Ubuntu20, Python3.8 is the default Python3. You can install the ability to make venvs with:
 
 .. code-block:: console
 
-    sudo apt install software-properties-common
-    sudo add-apt-repository ppa:deadsnakes/ppa
-    sudo apt install python3.8 python3.8-dev python3.8-venv
-
-This installs Python3.8, and also the ability to make virtual environments with python3.8-venv.
-You can now use your new version of Python3.8 by just typing 'python3.8' on the command line.
+    sudo apt install python3-dev python3-venv
 
-Now make the venv:
+And make and activate the venv:
 
 .. code-block:: console
 
-    python3.8 -m venv mainenv
+    python3 -m venv mainenv
     source mainenv/bin/activate
 
-This makes a virtual environment called 'mainenv' (first line) and then activates it (second line). If you close the terminal and open it again you would have to reactivate the virtual environment to make
-sure you are using the virtual environment version of Python3.8.
+This makes a virtual environment called 'mainenv' (first line) and then activates it (second line). If you close the
+terminal and open it again you would have to reactivate the virtual environment to make
+sure you are using the virtual environment version of Python3.10.
 
-On Ubuntu20, Python3.8 is the default Python3. You can install the ability to make venvs with:
+Ubuntu20 comes with Python 3.8 by default. Python 3.8 is sufficient for running RayFlare and necessary supporting packages,
+but if you want to update to a more recent Python version (3.10), this is easy:
 
 .. code-block:: console
 
-    sudo apt install python3-dev python3-venv
+    sudo apt install software-properties-common
+    sudo add-apt-repository ppa:deadsnakes/ppa
+    sudo apt install python3.10 python3.10-dev python3.10-venv
 
-And make and activate the venv:
+This installs Python3.10, and also the ability to make virtual environments with python3.10-venv.
+You can now use your new version of Python3.10 by just typing 'python3.10' on the command line.
+
+Now make the venv:
 
 .. code-block:: console
 
-    python3 -m venv mainenv
+    python3.10 -m venv mainenv
     source mainenv/bin/activate
 
-On MacOS, Homebrew Python (default version Python3.8) also comes with the venv ability.
+
+MacOS
+-------
+
+
+On MacOS, Homebrew Python (current default version Python3.10) also comes with the venv ability. This can be installed
+with:
+
+.. code-block:: console
+
+    brew install python

rayflare/matrix_formalism/multiply_matrices.py

@@ -302,7 +302,6 @@ def matrix_multiplication(bulk_mats, bulk_thick, options, layer_names, calc_prof
 
     len_calcs = np.array([len(x) if x is not None else 0 for x in calc_prof_list])
 
-
     if np.any(len_calcs > 0) or options.bulk_profile:
 
         a = [[] for _ in range(n_interfaces)]
@@ -420,6 +419,8 @@ def matrix_multiplication(bulk_mats, bulk_thick, options, layer_names, calc_prof
 
     else:
 
+        print("b")
+
         a = [[] for _ in range(n_interfaces)]
         vr = [[] for _ in range(n_bulks)]
         vt = [[] for _ in range(n_bulks)]

rayflare/transfer_matrix_method/tmm.py

@@ -477,6 +477,10 @@ def calculate_profile(layers):
                 output['A'] = 1 - out['R'] - out['T']
                 output['T'] = out['T']
                 output['A_per_layer'] = A_per_layer[1:-1]
+                output['vw_list'] = out['vw_list']
+                output['kz_list'] = out['kz_list']
+                output['th_list'] = out['th_list']
+
             else:
                 out = tmm.inc_tmm(pol, stack.get_indices(wavelength), stack.get_widths(), coherency_list, angle, wavelength)
                 A_per_layer = np.array(tmm.inc_absorp_in_each_layer(out))

setup.py

@@ -24,26 +24,6 @@ def gen_data_files(*dirs):
 config = ConfigParser()
 config.read([default_config])
 
-# Option for updating the manifest
-if "update_manifest" in sys.argv:
-    # Update the MANIFEST.in file with all the data from within solcore
-    include = "rayflare"
-    exclude = ["__pycache__", "egg", "darwin", "cpython"]
-    with open("MANIFEST.in", "w", encoding="utf-8") as f:
-        for root, dirs, files in os.walk("."):
-            if not any(sub in root for sub in exclude) and root[2:9] == include:
-                try:
-                    files.remove(".DS_Store")
-                except ValueError:
-                    pass
-                for file in files:
-                    if any(sub in file for sub in exclude):
-                        continue
-                    include_line = "include " + os.path.join(root[2:], file) + "\n"
-                    f.write(include_line)
-
-    sys.exit()
-
 # Get the long description from the README file
 with open(os.path.join(here, "README.md"), encoding="utf-8") as f:
     long_description = f.read()