Add effective area and temperature response (#33)

* Adding new filter naming method.

* Creating effective area preparatory code.

* Update channel.py

* Add channel test

* Adding temperature response

* Add data files for testing

* Adding CHIANTI geny data file

* Adding temperature response testing

* Adding util

* Deleting data

* Updating __init__.py

* Update xrtpy/response/channel.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/channel.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/channel.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <[email protected]>

* Delete un-used code.

* Update xrtpy/response/channel.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/channel.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/channel.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/channel.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/channel.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/channel.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/channel.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/channel.py

Co-authored-by: Nick Murphy <[email protected]>

* Made clarification to the testing script of the temperature response function.

* Cleared testing method for time script. Will update at a later time.

* A script for XRT date and time conversion to datetime objects.

* Creating a function to resolve filter name format inserted by user.

* Creating a observation date setter.

* Importing sunpy.time.

* Importing datetime

* Testing new mission date method.

* Correction to epoch.

* Minor changes to methods of problem solving.

* New script that only outputs the effective area.

* Test script for the new effective area script.

* Detail code review of the new effective area script.

* Add new effective area script and its corresponding attributes.

* Naming correction

* Corrections to import functions.

* Removed used effective area code.

* Updatig naming conventions.

* Testing edits.

* Updating effective area testing.

* Update temperature response testing functions.

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/effective_area.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/effective_area.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/effective_area.py

Co-authored-by: Nick Murphy <[email protected]>

* Clearing from used code.

* Updated effective area.

* Updated temperature response.

* Updated testing for channel.py.

* Updated testing for the effective area.

* Updated the CHIANTI file.

* Update xrtpy/response/effective_area.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/util/__init__ .py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/util/time.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/effective_area.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/effective_area.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/effective_area.py

Co-authored-by: Nick Murphy <[email protected]>

* Updating code methods.

* Clearing up code methods.

* Adding book reference.

* Cleaning up repeated code.

* Update xrtpy/response/effective_area.py

Co-authored-by: Nick Murphy <[email protected]>

* Cleaning up code.

* Updating ccd contam file.

* New updated temperature response IDL testing files.

* Updating testing methods.

* Updated testing for new IDL testing files.

* Updated test channel.

* Cleaned up channel code.

* Updated effective area testing.

* Updated effective area code.

* Reviewed with small updates.

* Deleting un-used temperature response IDL text testing files.

* Fixing spelling errors.

* Applied per-commit edits.

* Update xrtpy/response/channel.py

Co-authored-by: Nick Murphy <[email protected]>

* Converting string to f strings.

* Converting string to f strings.

* Updating geny files paths

* Updated geny file path

* Corrected imported functions

* Removing all code in test_time, not in use.

* Removed un-used function.

* Updated calling functions.

* Trying to fix failing issue.

* Trying to fix failing issue.

* Updated init file.

* Add empty list.

* Add empty list.

* Updated folder name

* Updated testing data path.

* Rename __init__.py to remove extra space

* Run pre-commit on all files

* Remove duplicate label

* Change formatting of codespell config

* Skip test collection in effective_area.py and temperature_response.py

Right now we're getting a weird error associated with test collection
for these two files, but I suspect it's not a problem with xrtpy itself.
I'm setting these two files to be ignored in pytest, and plan on
creating an issue for it.

* Apply pytest options

* Add pytest-allclose to test requirements

* Make Python tests {3.8, 3.9, 3.10} all be run at the same time

* Update xrtpy/response/channel.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/channel.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/effective_area.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/util/time.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/effective_area.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/effective_area.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/channel.py

Co-authored-by: Nick Murphy <[email protected]>

* Update xrtpy/response/effective_area.py

Co-authored-by: Nick Murphy <[email protected]>

* Added a doc string to a function.

* Added descriptions to the existing doc string.

* Update xrtpy/response/channel.py

Co-authored-by: Nick Murphy <[email protected]>

* Updated a for loop into an array.

* Updated code.

* Updated code.

Co-authored-by: Nick Murphy <[email protected]>

.github/workflows/testing.yml

@@ -19,6 +19,16 @@ jobs:
       matrix:
         include:
 
+        - name: Python 3.8 (Windows)
+          os: windows-latest
+          python: 3.8
+          noxenv: tests-3.8
+
+        - name: Python 3.9 (MacOS X)
+          os: ubuntu-latest
+          python: 3.9
+          noxenv: tests-3.9
+
         - name: Python 3.10
           noxenv: tests-3.10
           noxposargs: --durations=10
@@ -50,47 +60,6 @@ jobs:
     - name: ${{ matrix.name }}
       run: nox -s ${{ matrix.noxenv }} -- ${{ matrix.noxposargs }}
 
-  comprehensive-tests:
-
-    name: ${{ matrix.name }}
-    runs-on: ${{ matrix.os }}
-    needs: initial-tests
-    if: github.event.pull_request.draft == false
-
-    strategy:
-      fail-fast: false
-
-      matrix:
-        include:
-
-        - name: Python 3.8 (Windows)
-          os: windows-latest
-          python: 3.8
-          noxenv: tests-3.8
-
-        - name: Python 3.9 (MacOS X)
-          os: ubuntu-latest
-          python: 3.9
-          noxenv: tests-3.9
-
-    steps:
-
-    - name: Checkout code
-      uses: actions/checkout@v3
-      with:
-        fetch-depth: 0
-
-    - name: Set up Python
-      uses: actions/setup-python@v3
-      with:
-        python-version: ${{ matrix.python }}
-
-    - name: Install nox
-      run: python -m pip install --progress-bar off --upgrade nox
-
-    - name: ${{ matrix.name }}
-      run: nox -s ${{ matrix.noxenv }} -- ${{ matrix.noxposargs }}
-
   documentation:
 
     name: Documentation

docs/contributing/data_from_idl.rst

@@ -1,5 +1,3 @@
-.. _release guide:
-
 ********************************
 Updating Data from SolarSoft IDL
 ********************************

noxfile.py

@@ -11,12 +11,18 @@
 sphinx_no_notebooks = ["-D", "nbsphinx_execute=never"]
 sphinx_nitpicky = ["-n"]
 
+pytest_options = [
+    "--ignore",
+    "xrtpy/response/effective_area.py",
+    "--ignore",
+    "xrtpy/response/temperature_response.py",
+]
 
 @nox.session(python=python_versions)
 def tests(session):
     session.install("-r", "requirements/tests.txt")
     session.install(".")
-    session.run("pytest")
+    session.run("pytest", *pytest_options)
 
 
 @nox.session

requirements/tests.txt

@@ -11,4 +11,5 @@ flake8-rst-docstrings
 flake8-use-fstring
 pydocstyle
 pytest >= 5.4.0
+pytest-allclose
 pytest-xdist

setup.cfg

@@ -54,6 +54,7 @@ tests =
   flake8-use-fstring
   pydocstyle
   pytest >= 5.4.0
+  pytest-allclose
   pytest-xdist
 docs =
   # ought to mirror requirements/docs.txt
@@ -223,17 +224,7 @@ exclude_lines =
 
 [codespell]
 
-skip =
-  *.genx,
-  *.geny,
-  *.png,
-  *egg*,
-  .git,
-  .hypothesis,
-  .nox,
-  .tox,
-  __pycache__,
-  _build
+skip = *.genx,*.geny,*.png,*egg*,.git,.hypothesis,.nox,.tox,__pycache__,_build
 
 # Occasionally codespell will have false positives. Put words here that
 # should be ignored when codespell checks spellings.

xrtpy/__init__.py

@@ -5,10 +5,10 @@
 
 import warnings
 
-from . import response
+from xrtpy import response
 
 try:
-    from .version import __version__
+    from xrtpy.version import __version__
 except (ImportError, ModuleNotFoundError):
     warnings.warn("version not found.")
 

xrtpy/response/__init__.py

@@ -1,7 +1,17 @@
 """Response analysis for Hinode/XRT"""
 
-from . import channel
-from .channel import Geometry, EntranceFilter, Mirror, Filter, CCD, Channel, resolve_filter_name
+from xrtpy.response import channel, effective_area, temperature_response
+from xrtpy.response.channel import (
+    CCD,
+    Channel,
+    EntranceFilter,
+    Filter,
+    Geometry,
+    Mirror,
+    resolve_filter_name,
+)
+from xrtpy.response.effective_area import EffectiveAreaFundamental
+from xrtpy.response.temperature_response import TemperatureResponseFundamental
 
 __all__ = [
     "channel",
@@ -12,4 +22,8 @@
     "CCD",
     "Channel",
     "resolve_filter_name",
+    "EffectiveAreaFundamental",
+    "effective_area",
+    "temperature_response",
+    "TemperatureResponseFundamental",
 ]