Merge pull request #4 from saultyevil/develop

Update with new release

.readthedocs.yml

@@ -0,0 +1,29 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+    # You can also specify other tool versions:
+    # nodejs: "16"
+    # rust: "1.55"
+    # golang: "1.17"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/source/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: requirements.txt

docs/requirements.txt

@@ -0,0 +1,13 @@
+sphinx
+karma_sphinx_theme
+numpydoc
+numba==0.53.1
+numpy==1.20.2
+psutil==5.8.0
+SQLAlchemy==1.4.15
+matplotlib==3.3.4
+pandas==1.2.4
+dust_extinction==1.0
+scipy==1.6.2
+astropy==4.2.1
+protobuf==3.17.3

docs/source/modules.rst

@@ -9,68 +9,8 @@ pypython
 .. automodule:: pypython
     :members:
 
-math
-----
-
-.. automodule:: pypython.math
-    :members:
-
-math.vector
-^^^^^^^^^^^
-
-.. automodule:: pypython.math.vector
-    :members:
-
-physics
--------
-
-.. automodule:: pypython.physics
-    :members:
-
-physics.accretiondisc
-^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: pypython.physics.accretiondisc
-    :members:
-
-physics.blackbody
-^^^^^^^^^^^^^^^^^
-
-.. automodule:: pypython.physics.blackbody
-    :members:
-
-physics.blackhole
-^^^^^^^^^^^^^^^^^
-
-.. automodule:: pypython.physics.blackhole
-    :members:
-
-physics.models
-^^^^^^^^^^^^^^
-
-.. automodule:: pypython.physics.models
+.. automodule:: pypython.wind
     :members:
 
-plot
-----
-
-.. automodule:: pypython.plot
-    :members:
-
-plot.misc
-^^^^^^^^^
-
-.. automodule:: pypython.plot.misc
-    :members:
-
-plot.spectrum
-^^^^^^^^^^^^^
-
-.. automodule:: pypython.plot.spectrum
-    :members:
-
-plot.wind
-^^^^^^^^^
-
-.. automodule:: pypython.plot.wind
-    :members:
+.. automodule:: pypython.spectrum
+    :members:

pypython/__init__.py

@@ -5,6 +5,7 @@
 pypython is a companion python package to handle and analyse the data which
 comes out of a Python simulation.
 """
+
 import os.path
 import re
 import textwrap
@@ -16,13 +17,19 @@
 from subprocess import run
 
 import numpy as np
-from scipy.signal import boxcar, convolve
 
-from pypython.constants import (BOLTZMANN, CMS_TO_KMS, PARSEC, PI, PLANCK, VLIGHT)
-from pypython.error import RunError
-from pypython.math import vector
-from pypython.physics.blackhole import gravitational_radius
-from pypython.simulation.grid import get_parameter_value
+import pypython.constants as c
+import pypython.error as err
+import pypython.math
+import pypython.observations
+import pypython.physics
+import pypython.plot
+import pypython.simulation
+import pypython.spectrum
+import pypython.util
+import pypython.wind
+
+# Import all the things which will be able to be seen
 
 # Dictionary class -------------------------------------------------------------
 
@@ -165,13 +172,13 @@ def create_run_script(commands):
     file = "#!/bin/bash\n\ndeclare -a directories=(\n"
     for fp in paths:
         file += "\t\"{}\"\n".format(fp)
-    file += ")\n\ncfp=$(pfp)\nfor i in \"${directories[@]}\"\ndo\n\tcd $i\n\tpfp\n"
+    file += ")\n\ncwd=$(pwd)\nfor i in \"${directories[@]}\"\ndo\n\tcd $i\n\tpwd\n"
     if len(commands) > 1:
         for k in range(len(commands) - 1):
             file += "\t{}\n".format(commands[k + 1])
     else:
         file += "\t# commands\n"
-    file += "\tcd $cfp\ndone\n"
+    file += "\tcd $cwd\ndone\n"
 
     with open("commands.sh", "w") as f:
         f.write(file)
@@ -213,7 +220,6 @@ def create_slurm_file(name, n_cores, n_hours, n_minutes, py_flags, py_run_flags,
         module load conda/py3-latest
         source activate pypython
         python /home/ejp1n17/PythonScripts/pyrun -n {n_cores} {py_run_flags} -f='{py_flags}'
-        echo "Done!" > completed.txt
         """)
 
     if fp[-1] != "/":
@@ -255,7 +261,7 @@ def create_wind_save_tables(root, fp=".", ion_density=False, cell_spec=False, ve
     files_before = listdir(fp)
 
     if not Path(f"{fp}/data").exists():
-        run_command("Setup_Py_Dir", fp)
+        pypython.util.run_command("Setup_Py_Dir", fp)
 
     command = [name]
     if ion_density:
@@ -264,9 +270,9 @@ def create_wind_save_tables(root, fp=".", ion_density=False, cell_spec=False, ve
         command.append("-xall")
     command.append(root)
 
-    cmd = run_command(command, fp, verbose)
+    cmd = pypython.util.run_command(command, fp, verbose)
     if cmd.returncode != 0:
-        raise RunError(
+        raise err.RunError(
             f"windsave2table has failed to run, possibly due to an incompatible version\n{cmd.stdout.decode('utf-8')}")
 
     files_after = listdir(fp)
@@ -357,7 +363,7 @@ def get_python_version():
         The version string of the currently compiled Python.
     """
 
-    command = run_command(["py", "--version"])
+    command = pypython.util.run_command(["py", "--version"])
     stdout = command.stdout.decode("utf-8").split("\n")
     stderr = command.stderr.decode("utf-8")
 
@@ -467,6 +473,8 @@ def smooth_array(array, width):
     smoothed: np.ndarray
         The smoothed array
     """
+    from scipy.signal import boxcar, convolve
+
     if width is None or width == 0:
         return array
 
@@ -482,7 +490,7 @@ def run_py_optical_depth(root, photosphere=None, fp=".", verbose=False):
         command.append(f"-p {float(photosphere)}")
     command.append(root)
 
-    cmd = run_command(command, fp)
+    cmd = pypython.util.run_command(command, fp)
     stdout, stderr = cmd.stdout, cmd.stderr
 
     if verbose:
@@ -529,6 +537,9 @@ def run_py_wind(root, commands, fp="."):
 
 # Load in all the submodules ---------------------------------------------------
 
+Spectrum = pypython.spectrum.Spectrum
+Wind = pypython.wind.Wind
+
 __all__ = [
     # functions in pypython
     "check_sorted_array_ascending",
@@ -545,6 +556,7 @@ def run_py_wind(root, commands, fp="."):
     "run_py_optical_depth",
     "run_py_wind",
     # sub-modules
+    "dump",
     "math",
     "observations",
     "physics",
@@ -560,11 +572,4 @@ def run_py_wind(root, commands, fp="."):
     "constants"
 ]
 
-# These are put here to solve a circular dependency ----------------------------
-
-from pypython.plot import normalize_figure_style
-from pypython.spectrum import Spectrum
-from pypython.util import run_command
-from pypython.wind import Wind
-
-normalize_figure_style()
+pypython.plot.normalize_figure_style()