[MNT]: Release PR for first major release of fitter

.readthedocs.yml

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+version: 2
+
+formats:
+   - epub
+   - pdf
+
+build:
+  image: latest
+
+python:
+  version: 3.7
+#  install:
+#     - method: pip
+#       path: .
+#     - requirements: requirements.txt
+#  system_packages: true
+
+sphinx:
+  builder: html
+  configuration: docs/conf.py
+  fail_on_warning: true

.zenodo.json

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+{
+  "license": {
+  "id": "GPL-v3.0"
+  }, 
+  "notes": "When referencing this package, please cite the package DOI, the apexpy (10.5281/zenodo.1214206), flipchem (doi:10.5281/zenodo.3688853), and pymap3d (doi:10.5281/zenodo.595430).", 
+  "keywords": [
+    "Fitting Algorithm",
+    "Ionosphere",
+    "MSIS",
+    "AMISR",
+    "Incoherent Scatter Radar",
+    "Collective Thomson Scatter",
+    "Space Physics",
+    "Heliophysics"
+  ], 
+  "creators": [
+    {
+      "orcid": "0000-0001-8267-6327",
+      "name": "Michael Nicolls",
+    }
+    {
+      "orcid": "0000-0002-4621-3453",
+      "name": "Ashton S. Reimer"
+    },
+  ]
+}

README.rst

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+overspread
+==========
+This is the production version of the E and F region lagged product fitting software for the AMISRs. This work was supported by the National Science Foundation under cooperative agreement AGS–1840962.
+
+
+Overview
+--------
+Lorem Ipsum
+
+
+Quick Start
+-----------
+Lorem Ipsum
+
+
+Documentation
+-------------
+You can find more detailed documentation, including installation guides for macOS and Linux here: https://overspread.readthedocs.io
+
+
+
+References
+----------
+Lorem Ipsum

bin/example_config_exp.ini

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+[DEFAULT]
+YR = 2020/03
+DATAPATH = /path/to/rawfiles/20200324.010
+EXPDIR = MSWinds27H.v03
+EXPNAME = 20200324.010
+beamMapScaleFile = /path/to/cal-202003-calibration-ksys-03.21.2020.txt
+

bin/example_config_fit_ACfl.ini

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+[DEFAULT]
+INTEG = 10min
+
+[FIT_OPTIONS]
+DO_FITS = 1
+Recs2integrate = 60*10
+PERTURBATION_NOISE = 1
+procMedian = 1
+p_N0 = 1.0e11
+p_T0 = 1000.00
+p_M0 = 16.0
+SUMMATION_RULE = [[scipy.zeros(48),scipy.zeros(48)],[scipy.zeros(48)-1,scipy.zeros(48)],[scipy.zeros(48)-2,scipy.zeros(48)+1],[scipy.zeros(48)-4,scipy.zeros(48)+3]]
+fit0lag = 1 # whether to fit the 0 lag
+uselag1 = 1 # for density
+htmin = 80e3
+htmax = 350e3
+Ngroup = 4
+NION = 5
+molecularModel = 1
+mi = [16.0,32.0,30.0,28.0,14.0]
+GroupHt = [120e3,150e3,200e3,htmax]
+Ifit = [
+	[[-1,1,-2,1],[-2,-1,-2,-1],[-2,-1,-2,-1],[-2,-1,-2,-1],[-2,-1,-2,-1],[0,1,-2,-1]],
+	[[-1,1,-2,1],[-2,-1,-2,-1],[-2,-1,-2,-1],[-2,-1,-2,-1],[-2,-1,-2,-1],[0,1,-2,-1]],
+	[[-1,1,-2,1],[-2,-1,-2,-1],[-2,-1,-2,-1],[-2,-1,-2,-1],[-2,-1,-2,-1],[0,1,-2,-1]],
+	[[-1,1,-2,1],[-2,-1,-2,-1],[-2,-1,-2,-1],[-2,-1,-2,-1],[-2,-1,-2,-1],[0,1,-2,-1]]
+	]
+beamMapScale = 1
+fitcal = 1
+

bin/example_config_io_ACfl.ini

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+# This config file for I/O stuff, will vary from experiment to experiment
+
+[DEFAULT]
+
+ADDIT=
+OUTPUT_DAT_PATH=/path/to/output/directory/
+
+[INPUT]
+# Path to input filelist
+FILELIST=%(OUTPUT_DAT_PATH)s/%(YR)s/%(EXPDIR)s/%(EXPNAME)s/filelist_AC.txt
+
+# Path to files in filelist (if not absolute path)
+FILE_PATH=%(DATAPATH)s
+
+# Path to file containing lag ambiguity function
+#AMB_PATH = /path/to/AmbFunc.h5
+
+[OUTPUT]
+
+# Output path
+OUTPUT_PATH=%(OUTPUT_DAT_PATH)s/%(YR)s/%(EXPDIR)s/%(EXPNAME)s
+
+# Output filename
+OUTPUT_NAME=%(OUTPUT_PATH)s/%(EXPNAME)s_ac_%(INTEG)s%(ADDIT)s.h5
+
+proc_funcname=process_altcode
+h5DataPath=/IncohCodeFl/Data
+
+# 0 - none, 1 - fitted plots, 2 - fitted plots and iteration plots
+plotson=2
+nplots=1
+
+plotfrac=1
+
+plotsdir=%(OUTPUT_PATH)s/plots_ac_%(INTEG)s%(ADDIT)s
+saveplots=1
+
+xlims=[(0.01,10),(0,4),(-5,5)]

bin/run_AC.sh

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+#!/bin/sh
+
+FIT_CONFIG='config_fit_ACfl.ini'
+IO_CONFIG='config_io_ACfl.ini'
+
+if [ $# -gt 4 ] || [ $# -eq 0 ]; then
+    echo 1>&2 Usage: $0 RADAR EXPERIMENT [FIT_CONFIG] [IO_CONFIG]
+    echo 1>&2        Valid RADAR: pfisr, risrn, risrc, sondre
+    exit 127
+fi
+
+if [ $# -eq 3 ]; then
+    FIT_CONFIG=$3
+fi
+if [ $# -eq 2 ]; then
+    FIT_CONFIG=$3
+    IO_CONFIG=$4
+fi
+
+# configuration files
+configfiles="$FIT_CONFIG,$IO_CONFIG" # fit and io config files
+configexp="$2/config_exp.ini" # experiment specific config file(s)
+
+# run the fitter
+command="run_fitter $1 -c $configfiles,$configexp"
+echo $command
+$command

bin/run_LP.sh

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+#!/bin/sh
+
+FIT_CONFIG='config_fit_LP.ini'
+IO_CONFIG='config_io_LP.ini'
+
+if [ $# -gt 4 ] || [ $# -eq 0 ]; then
+    echo 1>&2 Usage: $0 RADAR EXPERIMENT [FIT_CONFIG] [IO_CONFIG]
+    echo 1>&2        Valid RADAR: pfisr, risrn, risrc, sondre
+    exit 127
+fi
+
+if [ $# -eq 3 ]; then
+    FIT_CONFIG=$3
+fi
+if [ $# -eq 2 ]; then
+    FIT_CONFIG=$3
+    IO_CONFIG=$4
+fi
+
+# configuration files
+configfiles="$FIT_CONFIG,$IO_CONFIG" # fit and io config files
+configexp="$2/config_exp.ini" # experiment specific config file(s)
+
+# run the fitter
+command="run_fitter $1 -c $configfiles,$configexp"
+echo $command
+$command