configs: Merge config specs into one single file

5 files changed, 235 insertions, 264 deletions

diff --git a/MANIFEST.in b/MANIFEST.in
index 10eb325..580f3cc 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,5 +1,5 @@
 include LICENSE
 include LICENSE-3RDPARTY
-include fg21sim/configs/*.conf.spec
+include fg21sim/configs/*.spec
 include fg21sim/webui/templates/*.html
 recursive-include fg21sim/webui/static *
diff --git a/fg21sim/configs/00-general.conf.spec b/fg21sim/configs/00-general.conf.spec
deleted file mode 100644
index 353e2cf..0000000
--- a/fg21sim/configs/00-general.conf.spec
+++ /dev/null
@@ -1,151 +0,0 @@
-# Configurations for "fg21sim"
-# -*- mode: conf -*-
-#
-# Syntax: `ConfigObj`, https://github.com/DiffSK/configobj
-#
-# This file contains the general configurations, which control the general
-# behaviors, or will be used in other configuration sections.
-
-
-# Foreground components to be simulated
-[foregrounds]
-# Diffuse Galactic synchrotron emission (unpolarized)
-galactic/synchrotron = boolean(default=False)
-
-# Diffuse Galactic free-free emission
-galactic/freefree = boolean(default=False)
-
-# Galactic supernova remnants emission
-galactic/snr = boolean(default=False)
-
-#  Extragalactic clusters of galaxies emission
-extragalactic/clusters = boolean(default=False)
-
-# Emission from multiple types of extragalactic point sources
-# NOTE: This component is not well integrated and tested at the moment
-extragalactic/pointsources = boolean(default=False)
-
-
-# Simulation sky/region configurations
-[sky]
-# Type of the input/output simulation sky
-# + patch:
-#       Input/output sky template is only a (square) patch of the sky.
-#       The simulated output maps have the same coverage/field as the
-#       input template, as well as the coordinate projection.
-# + healpix:
-#       Input/output sky template covers (almost) all sky, and stored
-#       in HEALPix format.  The simulated output maps will also be
-#       all-sky using the HEALPix projection.
-type = option("patch", "healpix", default="patch")
-
-  # Configurations for input/output sky patch
-  [[patch]]
-  # The (R.A., Dec.) coordinate of the sky patch center
-  # Unit: [deg]
-  # (MWA EoR0 field center: (0, -27))
-  xcenter = float(default=0.0, min=0.0, max=360.0)
-  ycenter = float(default=-27.0, min=-90.0, max=90.0)
-
-  # The image dimensions (i.e., number of pixels) of the sky patch,
-  # along the X (R.A./longitude) and Y (Dec./latitude) axes.
-  # Default: 1800x1800 => 10x10 [deg^2] (20 arcsec/pixel)
-  xsize = integer(default=1800, min=1)
-  ysize = integer(default=1800, min=1)
-
-  # Pixel size [arcsec]
-  pixelsize = float(default=20.0, min=0.0)
-
-  # Configurations for input/output HEALPix sky
-  [[healpix]]
-  # HEALPix Nside value, i.e., pixel resolution
-  nside = integer(default=1024, min=128)
-
-
-# Frequencies specification of the simulation products
-[frequency]
-# How to specify the frequencies
-# + custom:
-#       directly specify the frequency values using the "frequencies" config
-# + calc:
-#       calculate the frequency values by "start", "stop", and "step"
-type = option("custom", "calc", default="custom")
-
-# The frequency values to be simulated if above "type" is "custom".
-# Unit: [MHz]
-frequencies = float_list(default=list())
-
-# Parameters to calculate the frequencies
-# NOTE: "start" and "stop" frequencies are both inclusive.
-# Unit: [MHz]
-start = float(default=None, min=0.0)
-stop = float(default=None, min=0.0)
-step = float(default=None, min=0.0)
-
-
-# Configuration for output products
-[output]
-# Filename pattern for the output products, which will be finally
-# formatted using `str.format()`.
-filename_pattern = string(default="{prefix}_{frequency:06.2f}.fits")
-
-# Use single-precision float instead of double (to save spaces)
-float32 = boolean(default=True)
-
-# Whether to calculate the checksum for the output FITS file?
-# NOTE: May cost significantly more time on writing FITS file.
-checksum = boolean(default=False)
-
-# Whether to overwrite existing files (e.g., maps, catalogs, manifest, ...)
-clobber = boolean(default=False)
-
-# Filename of the simulation products manifest (JSON format), which
-# records all output products together with their sizes and MD5 hashes.
-# Do not create such a manifest if this option is not specified.
-manifest = string(default=None)
-
-
-# Cosmological parameters
-# References: Komatsu et al. 2011, ApJS, 192, 18; Tab.(1)
-[cosmology]
-# Hubble constant at z=0; [km/s/Mpc]
-H0 = float(default=71.0, min=0.0)
-# Density of non-relativistic matter in units of the critical density at z=0
-OmegaM0 = float(default=0.27, min=0.0, max=1.0)
-# Density of the baryon at present day
-Omegab0 = float(default=0.046, min=0.0, max=1.0)
-# Present-day CMB temperature; [K]
-Tcmb0 = float(default=2.725)
-# Present-day rms density fluctuations on a scale of 8 h^-1 [Mpc]
-sigma8 = float(default=0.81, min=0.0)
-# Scalar spectral index
-ns = float(default=0.96, min=0.0)
-
-
-# Configurations for initialization/reconfiguration of the `logging` module
-[logging]
-# debug:    Detailed information, typically of interest only when diagnosing
-#           problems.
-# info:     Confirmation that things are working as expected.
-# warning:  An indication that something unexpected happended, or indicative
-#           of some problem in the near future (e.g., "disk space low").
-#           The software is still working as expected.
-# error:    Due to a more serious problem, the software has not been able to
-#           perform some function.
-# critical: A serious error, indicating that the program itself may be unable
-#           to continue running.
-level = option("debug", "info", "warning", "error", "critical", default="info")
-
-# Set the format of displayed messages
-format = string(default="%(asctime)s [%(levelname)s] <%(name)s:%(lineno)d> %(message)s")
-
-# Set the date/time format in messages
-datefmt = string(default="%H:%M:%S")
-
-# Set the logging filename (will create a `FileHandler`)
-# If set to "" (empty string), then the `FileHandler` will be disabled.
-filename = string(default="")
-
-# Set the stream used to initialize the `StreamHandler`
-# If set to "" (empty string), then the `StreamHandler` will be disabled.
-stream = option("stderr", "stdout", "", default="stderr")
diff --git a/fg21sim/configs/10-galactic.conf.spec b/fg21sim/configs/10-galactic.conf.spec
deleted file mode 100644
index 9185dc0..0000000
--- a/fg21sim/configs/10-galactic.conf.spec
+++ /dev/null
@@ -1,89 +0,0 @@
-# Configurations for "fg21sim"
-# -*- mode: conf -*-
-#
-# Syntax: `ConfigObj`, https://github.com/DiffSK/configobj
-#
-# This file contains the options corresponding the Galactic emission
-# components, which currently includes the following components:
-# - synchrotron
-# - freefree
-# - snr
-
-
-[galactic]
-
-  # Synchrotron emission component (unpolarized)
-  [[synchrotron]]
-  # The template map for the simulation, e.g., Haslam 408 MHz survey.
-  # Unit: [K] (Kelvin)
-  template = string(default=None)
-  # The frequency of the template map.
-  # Unit: [MHz]
-  template_freq = float(default=None, min=0.0)
-
-  # Spectral index map
-  indexmap = string(default=None)
-
-  # Whether add fluctuations on the small scales according the angular
-  # power spectrum prediction?
-  add_smallscales = boolean(default=False)
-  # Range of multipole moments (l) of the angular power spectrum.
-  # The power spectrum will be cut off to a constant for multipole l < lmin.
-  # NOTE: Update the ``lmax`` accordingly w.r.t. ``sky/healpix/nside``.
-  #       Generally, lmax = 3 * nside - 1
-  lmin = integer(min=0, default=10)
-  lmax = integer(min=1, default=3071)
-
-  # Filename prefix for this component
-  prefix = string(default="gsync")
-  # Output directory to save the simulated results
-  output_dir = string(default=None)
-
-  # Free-free bremsstrahlung emission component
-  [[freefree]]
-  # The Hα map from which to derive the free-free emission
-  # Unit: [Rayleigh]
-  halphamap = string(default=None)
-
-  # The 100-μm dust map used to correct Hα dust absorption
-  # Unit: [MJy/sr]
-  dustmap = string(default=None)
-
-  # Effective dust fraction in the LoS actually absorbing Halpha
-  dust_fraction = float(default=0.33, min=0.1, max=1.0)
-
-  # Halpha absorption threshold:
-  # When the dust absorption goes rather large, the true Halpha
-  # absorption can not well determined.  This configuration sets the
-  # threshold below which the dust absorption can be well determined,
-  # while the sky regions with higher absorption are masked out due
-  # to unreliable absorption correction.
-  # Unit: [mag]
-  halpha_abs_th = float(default=1.0)
-
-  # The electron temperature assumed for the ionized interstellar medium
-  # that generating H{\alpha} emission.
-  # Unit: [K]
-  electron_temperature = float(default=7000.0, min=1000)
-
-  # Filename prefix for this component
-  prefix = string(default="gfree")
-  # Output directory to save the simulated results
-  output_dir = string(default=None)
-
-  # Supernova remnants emission
-  [[snr]]
-  # The Galactic SNRs catalog data (CSV file)
-  catalog = string(default=None)
-  # Output the effective/inuse SNRs catalog data (CSV file)
-  catalog_outfile = string(default=None)
-
-  # Resolution for simulating each SNR template, which are finally
-  # mapped to the all-sky HEALPix map if used.
-  # Unit: [arcsec]
-  resolution = float(default=30.0, min=5.0)
-
-  # Filename prefix for this component
-  prefix = string(default="gsnr")
-  # Output directory to save the simulated results
-  output_dir = string(default=None)
diff --git a/fg21sim/configs/20-extragalactic.conf.spec b/fg21sim/configs/config.spec
index 943c7e0..6b871e4 100644
--- a/fg21sim/configs/20-extragalactic.conf.spec
+++ b/fg21sim/configs/config.spec
@@ -1,14 +1,240 @@
-# Configurations for "fg21sim"
-# -*- mode: conf -*-
 #
+# Configurations for "fg21sim"
 # Syntax: `ConfigObj`, https://github.com/DiffSK/configobj
 #
-# This file contains the options corresponding the extragalactic emission
-# components, which currently includes the following components:
-# - clusters: halos
-# - pointsources
 
 
+# Foreground components to be simulated
+[foregrounds]
+# Diffuse Galactic synchrotron emission (unpolarized)
+galactic/synchrotron = boolean(default=False)
+
+# Diffuse Galactic free-free emission
+galactic/freefree = boolean(default=False)
+
+# Galactic supernova remnants emission
+galactic/snr = boolean(default=False)
+
+#  Extragalactic clusters of galaxies emission
+extragalactic/clusters = boolean(default=False)
+
+# Emission from multiple types of extragalactic point sources
+# NOTE: This component is not well integrated and tested at the moment
+extragalactic/pointsources = boolean(default=False)
+
+
+# Simulation sky/region configurations
+[sky]
+# Type of the input/output simulation sky
+# + patch:
+#       Input/output sky template is only a (square) patch of the sky.
+#       The simulated output maps have the same coverage/field as the
+#       input template, as well as the coordinate projection.
+# + healpix:
+#       Input/output sky template covers (almost) all sky, and stored
+#       in HEALPix format.  The simulated output maps will also be
+#       all-sky using the HEALPix projection.
+type = option("patch", "healpix", default="patch")
+
+  # Configurations for input/output sky patch
+  [[patch]]
+  # The (R.A., Dec.) coordinate of the sky patch center
+  # Unit: [deg]
+  # (MWA EoR0 field center: (0, -27))
+  xcenter = float(default=0.0, min=0.0, max=360.0)
+  ycenter = float(default=-27.0, min=-90.0, max=90.0)
+
+  # The image dimensions (i.e., number of pixels) of the sky patch,
+  # along the X (R.A./longitude) and Y (Dec./latitude) axes.
+  # Default: 1800x1800 => 10x10 [deg^2] (20 arcsec/pixel)
+  xsize = integer(default=1800, min=1)
+  ysize = integer(default=1800, min=1)
+
+  # Pixel size [arcsec]
+  pixelsize = float(default=20.0, min=0.0)
+
+  # Configurations for input/output HEALPix sky
+  [[healpix]]
+  # HEALPix Nside value, i.e., pixel resolution
+  nside = integer(default=1024, min=128)
+
+
+# Frequencies specification of the simulation products
+[frequency]
+# How to specify the frequencies
+# + custom:
+#       directly specify the frequency values using the "frequencies" config
+# + calc:
+#       calculate the frequency values by "start", "stop", and "step"
+type = option("custom", "calc", default="custom")
+
+# The frequency values to be simulated if above "type" is "custom".
+# Unit: [MHz]
+frequencies = float_list(default=list())
+
+# Parameters to calculate the frequencies
+# NOTE: "start" and "stop" frequencies are both inclusive.
+# Unit: [MHz]
+start = float(default=None, min=0.0)
+stop = float(default=None, min=0.0)
+step = float(default=None, min=0.0)
+
+
+# Configuration for output products
+[output]
+# Filename pattern for the output products, which will be finally
+# formatted using `str.format()`.
+filename_pattern = string(default="{prefix}_{frequency:06.2f}.fits")
+
+# Use single-precision float instead of double (to save spaces)
+float32 = boolean(default=True)
+
+# Whether to calculate the checksum for the output FITS file?
+# NOTE: May cost significantly more time on writing FITS file.
+checksum = boolean(default=False)
+
+# Whether to overwrite existing files (e.g., maps, catalogs, manifest, ...)
+clobber = boolean(default=False)
+
+# Filename of the simulation products manifest (JSON format), which
+# records all output products together with their sizes and MD5 hashes.
+# Do not create such a manifest if this option is not specified.
+manifest = string(default=None)
+
+
+# Cosmological parameters
+# References: Komatsu et al. 2011, ApJS, 192, 18; Tab.(1)
+[cosmology]
+# Hubble constant at z=0; [km/s/Mpc]
+H0 = float(default=71.0, min=0.0)
+# Density of non-relativistic matter in units of the critical density at z=0
+OmegaM0 = float(default=0.27, min=0.0, max=1.0)
+# Density of the baryon at present day
+Omegab0 = float(default=0.046, min=0.0, max=1.0)
+# Present-day CMB temperature; [K]
+Tcmb0 = float(default=2.725)
+# Present-day rms density fluctuations on a scale of 8 h^-1 [Mpc]
+sigma8 = float(default=0.81, min=0.0)
+# Scalar spectral index
+ns = float(default=0.96, min=0.0)
+
+
+# Configurations for initialization/reconfiguration of the `logging` module
+[logging]
+# debug:    Detailed information, typically of interest only when diagnosing
+#           problems.
+# info:     Confirmation that things are working as expected.
+# warning:  An indication that something unexpected happended, or indicative
+#           of some problem in the near future (e.g., "disk space low").
+#           The software is still working as expected.
+# error:    Due to a more serious problem, the software has not been able to
+#           perform some function.
+# critical: A serious error, indicating that the program itself may be unable
+#           to continue running.
+level = option("debug", "info", "warning", "error", "critical", default="info")
+
+# Set the format of displayed messages
+format = string(default="%(asctime)s [%(levelname)s] <%(name)s:%(lineno)d> %(message)s")
+
+# Set the date/time format in messages
+datefmt = string(default="%H:%M:%S")
+
+# Set the logging filename (will create a `FileHandler`)
+# If set to "" (empty string), then the `FileHandler` will be disabled.
+filename = string(default="")
+
+# Set the stream used to initialize the `StreamHandler`
+# If set to "" (empty string), then the `StreamHandler` will be disabled.
+stream = option("stderr", "stdout", "", default="stderr")
+
+
+#
+# Galactic emission components
+#
+
+[galactic]
+
+  # Synchrotron emission component (unpolarized)
+  [[synchrotron]]
+  # The template map for the simulation, e.g., Haslam 408 MHz survey.
+  # Unit: [K] (Kelvin)
+  template = string(default=None)
+  # The frequency of the template map.
+  # Unit: [MHz]
+  template_freq = float(default=None, min=0.0)
+
+  # Spectral index map
+  indexmap = string(default=None)
+
+  # Whether add fluctuations on the small scales according the angular
+  # power spectrum prediction?
+  add_smallscales = boolean(default=False)
+  # Range of multipole moments (l) of the angular power spectrum.
+  # The power spectrum will be cut off to a constant for multipole l < lmin.
+  # NOTE: Update the ``lmax`` accordingly w.r.t. ``sky/healpix/nside``.
+  #       Generally, lmax = 3 * nside - 1
+  lmin = integer(min=0, default=10)
+  lmax = integer(min=1, default=3071)
+
+  # Filename prefix for this component
+  prefix = string(default="gsync")
+  # Output directory to save the simulated results
+  output_dir = string(default=None)
+
+  # Free-free bremsstrahlung emission component
+  [[freefree]]
+  # The Hα map from which to derive the free-free emission
+  # Unit: [Rayleigh]
+  halphamap = string(default=None)
+
+  # The 100-μm dust map used to correct Hα dust absorption
+  # Unit: [MJy/sr]
+  dustmap = string(default=None)
+
+  # Effective dust fraction in the LoS actually absorbing Halpha
+  dust_fraction = float(default=0.33, min=0.1, max=1.0)
+
+  # Halpha absorption threshold:
+  # When the dust absorption goes rather large, the true Halpha
+  # absorption can not well determined.  This configuration sets the
+  # threshold below which the dust absorption can be well determined,
+  # while the sky regions with higher absorption are masked out due
+  # to unreliable absorption correction.
+  # Unit: [mag]
+  halpha_abs_th = float(default=1.0)
+
+  # The electron temperature assumed for the ionized interstellar medium
+  # that generating H{\alpha} emission.
+  # Unit: [K]
+  electron_temperature = float(default=7000.0, min=1000)
+
+  # Filename prefix for this component
+  prefix = string(default="gfree")
+  # Output directory to save the simulated results
+  output_dir = string(default=None)
+
+  # Supernova remnants emission
+  [[snr]]
+  # The Galactic SNRs catalog data (CSV file)
+  catalog = string(default=None)
+  # Output the effective/inuse SNRs catalog data (CSV file)
+  catalog_outfile = string(default=None)
+
+  # Resolution for simulating each SNR template, which are finally
+  # mapped to the all-sky HEALPix map if used.
+  # Unit: [arcsec]
+  resolution = float(default=30.0, min=5.0)
+
+  # Filename prefix for this component
+  prefix = string(default="gsnr")
+  # Output directory to save the simulated results
+  output_dir = string(default=None)
+
+
+#
+# Extragalactic emission components
+#
+
 [extragalactic]
   #
   # Press-Schechter formalism to determine the cluster distributions
diff --git a/fg21sim/configs/manager.py b/fg21sim/configs/manager.py
index e2103da..07f6f77 100644
--- a/fg21sim/configs/manager.py
+++ b/fg21sim/configs/manager.py
@@ -31,22 +31,6 @@ from ..errors import ConfigError
 logger = logging.getLogger(__name__)
 
 
-def _get_configspec():
-    """Found and read all the configuration specifications"""
-    files = sorted(pkg_resources.resource_listdir(__name__, ""))
-    specfiles = [fn for fn in files if fn.endswith(".conf.spec")]
-    if os.environ.get("DEBUG_FG21SIM"):
-        print("DEBUG: Found config specifications: %s" % ", ".join(specfiles),
-              file=sys.stderr)
-    # NOTE:
-    # `resource_string()` returns the resource in *binary/bytes* string
-    configspec = "\n".join([
-        pkg_resources.resource_string(__name__, fn).decode("utf-8")
-        for fn in specfiles
-    ]).split("\n")
-    return configspec
-
-
 def _flatten_dict(d, sep="/", parent_key=""):
     """
     Recursively flatten a nested dictionary with keys compressed.
@@ -147,7 +131,8 @@ class ConfigManager:
         If the ``userconfig`` provided, the user configurations is also
         loaded, validated, and merged.
         """
-        configspec = _get_configspec()
+        configspec = pkg_resources.resource_string(
+                __name__, "config.spec").decode("utf-8")
         self._configspec = ConfigObj(configspec, interpolation=False,
                                      list_values=False, _inspec=True,
                                      encoding="utf-8")