From 3ee22ce3b1ae29514e3efa89a3c6a3304f22335d Mon Sep 17 00:00:00 2001 From: Maxwlel Date: Sun, 16 Jun 2024 11:32:22 -0400 Subject: [PATCH 1/6] target completeness caching --- .venv/bin/Activate.ps1 | 241 ++++++++++++++++++ .venv/bin/activate | 66 +++++ .venv/bin/activate.csh | 25 ++ .venv/bin/activate.fish | 64 +++++ .venv/bin/pip | 8 + .venv/bin/pip3 | 8 + .venv/bin/pip3.9 | 8 + .venv/bin/python | 1 + .venv/bin/python3 | 1 + .venv/bin/python3.9 | 1 + .venv/pyvenv.cfg | 3 + EXOSIMS/Completeness/GarrettCompleteness.py | 164 ++++++++---- ...s.TestBackgroundSources-20240612212837.xml | 11 + ...rrett.TestBrownvGarrett-20240613191607.xml | 11 + ...rrett.TestBrownvGarrett-20240613191619.xml | 11 + ...rrett.TestBrownvGarrett-20240613192133.xml | 42 +++ ...rrett.TestBrownvGarrett-20240613192645.xml | 45 ++++ ...rrett.TestBrownvGarrett-20240613192747.xml | 45 ++++ ...rrett.TestBrownvGarrett-20240613192910.xml | 45 ++++ ...rrett.TestBrownvGarrett-20240613193030.xml | 45 ++++ 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...rrett.TestBrownvGarrett-20240613204842.xml | 32 +++ ...rrett.TestBrownvGarrett-20240613204915.xml | 32 +++ ...rrett.TestBrownvGarrett-20240613205326.xml | 32 +++ ...rrett.TestBrownvGarrett-20240613205437.xml | 32 +++ ...rrett.TestBrownvGarrett-20240613205524.xml | 32 +++ ...rrett.TestBrownvGarrett-20240613205619.xml | 41 +++ ...rrett.TestBrownvGarrett-20240613205801.xml | 42 +++ ...rrett.TestBrownvGarrett-20240613210040.xml | 42 +++ ...rrett.TestBrownvGarrett-20240613210301.xml | 40 +++ ...rrett.TestBrownvGarrett-20240613210425.xml | 40 +++ ...rrett.TestBrownvGarrett-20240613210444.xml | 36 +++ ...rrett.TestBrownvGarrett-20240613212216.xml | 44 ++++ ...rrett.TestBrownvGarrett-20240613212317.xml | 43 ++++ ...rrett.TestBrownvGarrett-20240613212510.xml | 45 ++++ ...rrett.TestBrownvGarrett-20240613222132.xml | 38 +++ ...rrett.TestBrownvGarrett-20240613222357.xml | 39 +++ ...rrett.TestBrownvGarrett-20240613222533.xml | 42 +++ ...rrett.TestBrownvGarrett-20240613222702.xml | 49 ++++ ...rrett.TestBrownvGarrett-20240613222850.xml | 37 +++ ...rrett.TestBrownvGarrett-20240613222938.xml | 37 +++ ...rrett.TestBrownvGarrett-20240613223001.xml | 54 ++++ ...rrett.TestBrownvGarrett-20240613223330.xml | 11 + ...rrett.TestBrownvGarrett-20240613223346.xml | 43 ++++ ...rrett.TestBrownvGarrett-20240613223405.xml | 43 ++++ ...rrett.TestBrownvGarrett-20240613223429.xml | 122 +++++++++ ...rrett.TestBrownvGarrett-20240613223517.xml | 47 ++++ ...rrett.TestBrownvGarrett-20240614220203.xml | 47 ++++ ...rrett.TestBrownvGarrett-20240614231320.xml | 57 +++++ ...rrett.TestBrownvGarrett-20240614231935.xml | 47 ++++ ...test.loader._FailedTest-20240612212614.xml | 19 ++ ...test.loader._FailedTest-20240613191413.xml | 19 ++ ...test.loader._FailedTest-20240613191513.xml | 19 ++ ...test.loader._FailedTest-20240613191534.xml | 19 ++ tests/Completeness/test_BrownvGarrett.py | 5 +- 71 files changed, 3092 insertions(+), 58 deletions(-) create mode 100644 .venv/bin/Activate.ps1 create mode 100644 .venv/bin/activate create mode 100644 .venv/bin/activate.csh create mode 100644 .venv/bin/activate.fish create mode 100755 .venv/bin/pip create mode 100755 .venv/bin/pip3 create mode 100755 .venv/bin/pip3.9 create mode 120000 .venv/bin/python create mode 120000 .venv/bin/python3 create mode 120000 .venv/bin/python3.9 create mode 100644 .venv/pyvenv.cfg create mode 100644 test-reports/TEST-tests.BackgroundSources.test_BackgroundSources.TestBackgroundSources-20240612212837.xml create mode 100644 test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613191607.xml create mode 100644 test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613191619.xml create mode 100644 test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613192133.xml create mode 100644 test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613192645.xml create mode 100644 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create mode 100644 test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613223429.xml create mode 100644 test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613223517.xml create mode 100644 test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240614220203.xml create mode 100644 test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240614231320.xml create mode 100644 test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240614231935.xml create mode 100644 test-reports/TEST-unittest.loader._FailedTest-20240612212614.xml create mode 100644 test-reports/TEST-unittest.loader._FailedTest-20240613191413.xml create mode 100644 test-reports/TEST-unittest.loader._FailedTest-20240613191513.xml create mode 100644 test-reports/TEST-unittest.loader._FailedTest-20240613191534.xml diff --git a/.venv/bin/Activate.ps1 b/.venv/bin/Activate.ps1 new file mode 100644 index 000000000..2fb3852c3 --- /dev/null +++ b/.venv/bin/Activate.ps1 @@ -0,0 +1,241 @@ +<# +.Synopsis +Activate a Python virtual environment for the current PowerShell session. + +.Description +Pushes the python executable for a virtual environment to the front of the +$Env:PATH environment variable and sets the prompt to signify that you are +in a Python virtual environment. Makes use of the command line switches as +well as the `pyvenv.cfg` file values present in the virtual environment. + +.Parameter VenvDir +Path to the directory that contains the virtual environment to activate. The +default value for this is the parent of the directory that the Activate.ps1 +script is located within. + +.Parameter Prompt +The prompt prefix to display when this virtual environment is activated. By +default, this prompt is the name of the virtual environment folder (VenvDir) +surrounded by parentheses and followed by a single space (ie. '(.venv) '). + +.Example +Activate.ps1 +Activates the Python virtual environment that contains the Activate.ps1 script. + +.Example +Activate.ps1 -Verbose +Activates the Python virtual environment that contains the Activate.ps1 script, +and shows extra information about the activation as it executes. + +.Example +Activate.ps1 -VenvDir C:\Users\MyUser\Common\.venv +Activates the Python virtual environment located in the specified location. + +.Example +Activate.ps1 -Prompt "MyPython" +Activates the Python virtual environment that contains the Activate.ps1 script, +and prefixes the current prompt with the specified string (surrounded in +parentheses) while the virtual environment is active. + +.Notes +On Windows, it may be required to enable this Activate.ps1 script by setting the +execution policy for the user. You can do this by issuing the following PowerShell +command: + +PS C:\> Set-ExecutionPolicy -ExecutionPolicy RemoteSigned -Scope CurrentUser + +For more information on Execution Policies: +https://go.microsoft.com/fwlink/?LinkID=135170 + +#> +Param( + [Parameter(Mandatory = $false)] + [String] + $VenvDir, + [Parameter(Mandatory = $false)] + [String] + $Prompt +) + +<# Function declarations --------------------------------------------------- #> + +<# +.Synopsis +Remove all shell session elements added by the Activate script, including the +addition of the virtual environment's Python executable from the beginning of +the PATH variable. + +.Parameter NonDestructive +If present, do not remove this function from the global namespace for the +session. + +#> +function global:deactivate ([switch]$NonDestructive) { + # Revert to original values + + # The prior prompt: + if (Test-Path -Path Function:_OLD_VIRTUAL_PROMPT) { + Copy-Item -Path Function:_OLD_VIRTUAL_PROMPT -Destination Function:prompt + Remove-Item -Path Function:_OLD_VIRTUAL_PROMPT + } + + # The prior PYTHONHOME: + if (Test-Path -Path Env:_OLD_VIRTUAL_PYTHONHOME) { + Copy-Item -Path Env:_OLD_VIRTUAL_PYTHONHOME -Destination Env:PYTHONHOME + Remove-Item -Path Env:_OLD_VIRTUAL_PYTHONHOME + } + + # The prior PATH: + if (Test-Path -Path Env:_OLD_VIRTUAL_PATH) { + Copy-Item -Path Env:_OLD_VIRTUAL_PATH -Destination Env:PATH + Remove-Item -Path Env:_OLD_VIRTUAL_PATH + } + + # Just remove the VIRTUAL_ENV altogether: + if (Test-Path -Path Env:VIRTUAL_ENV) { + Remove-Item -Path env:VIRTUAL_ENV + } + + # Just remove the _PYTHON_VENV_PROMPT_PREFIX altogether: + if (Get-Variable -Name "_PYTHON_VENV_PROMPT_PREFIX" -ErrorAction SilentlyContinue) { + Remove-Variable -Name _PYTHON_VENV_PROMPT_PREFIX -Scope Global -Force + } + + # Leave deactivate function in the global namespace if requested: + if (-not $NonDestructive) { + Remove-Item -Path function:deactivate + } +} + +<# +.Description +Get-PyVenvConfig parses the values from the pyvenv.cfg file located in the +given folder, and returns them in a map. + +For each line in the pyvenv.cfg file, if that line can be parsed into exactly +two strings separated by `=` (with any amount of whitespace surrounding the =) +then it is considered a `key = value` line. The left hand string is the key, +the right hand is the value. + +If the value starts with a `'` or a `"` then the first and last character is +stripped from the value before being captured. + +.Parameter ConfigDir +Path to the directory that contains the `pyvenv.cfg` file. +#> +function Get-PyVenvConfig( + [String] + $ConfigDir +) { + Write-Verbose "Given ConfigDir=$ConfigDir, obtain values in pyvenv.cfg" + + # Ensure the file exists, and issue a warning if it doesn't (but still allow the function to continue). + $pyvenvConfigPath = Join-Path -Resolve -Path $ConfigDir -ChildPath 'pyvenv.cfg' -ErrorAction Continue + + # An empty map will be returned if no config file is found. + $pyvenvConfig = @{ } + + if ($pyvenvConfigPath) { + + Write-Verbose "File exists, parse `key = value` lines" + $pyvenvConfigContent = Get-Content -Path $pyvenvConfigPath + + $pyvenvConfigContent | ForEach-Object { + $keyval = $PSItem -split "\s*=\s*", 2 + if ($keyval[0] -and $keyval[1]) { + $val = $keyval[1] + + # Remove extraneous quotations around a string value. + if ("'""".Contains($val.Substring(0, 1))) { + $val = $val.Substring(1, $val.Length - 2) + } + + $pyvenvConfig[$keyval[0]] = $val + Write-Verbose "Adding Key: '$($keyval[0])'='$val'" + } + } + } + return $pyvenvConfig +} + + +<# Begin Activate script --------------------------------------------------- #> + +# Determine the containing directory of this script +$VenvExecPath = Split-Path -Parent $MyInvocation.MyCommand.Definition +$VenvExecDir = Get-Item -Path $VenvExecPath + +Write-Verbose "Activation script is located in path: '$VenvExecPath'" +Write-Verbose "VenvExecDir Fullname: '$($VenvExecDir.FullName)" +Write-Verbose "VenvExecDir Name: '$($VenvExecDir.Name)" + +# Set values required in priority: CmdLine, ConfigFile, Default +# First, get the location of the virtual environment, it might not be +# VenvExecDir if specified on the command line. +if ($VenvDir) { + Write-Verbose "VenvDir given as parameter, using '$VenvDir' to determine values" +} +else { + Write-Verbose "VenvDir not given as a parameter, using parent directory name as VenvDir." + $VenvDir = $VenvExecDir.Parent.FullName.TrimEnd("\\/") + Write-Verbose "VenvDir=$VenvDir" +} + +# Next, read the `pyvenv.cfg` file to determine any required value such +# as `prompt`. +$pyvenvCfg = Get-PyVenvConfig -ConfigDir $VenvDir + +# Next, set the prompt from the command line, or the config file, or +# just use the name of the virtual environment folder. +if ($Prompt) { + Write-Verbose "Prompt specified as argument, using '$Prompt'" +} +else { + Write-Verbose "Prompt not specified as argument to script, checking pyvenv.cfg value" + if ($pyvenvCfg -and $pyvenvCfg['prompt']) { + Write-Verbose " Setting based on value in pyvenv.cfg='$($pyvenvCfg['prompt'])'" + $Prompt = $pyvenvCfg['prompt']; + } + else { + Write-Verbose " Setting prompt based on parent's directory's name. (Is the directory name passed to venv module when creating the virutal environment)" + Write-Verbose " Got leaf-name of $VenvDir='$(Split-Path -Path $venvDir -Leaf)'" + $Prompt = Split-Path -Path $venvDir -Leaf + } +} + +Write-Verbose "Prompt = '$Prompt'" +Write-Verbose "VenvDir='$VenvDir'" + +# Deactivate any currently active virtual environment, but leave the +# deactivate function in place. +deactivate -nondestructive + +# Now set the environment variable VIRTUAL_ENV, used by many tools to determine +# that there is an activated venv. +$env:VIRTUAL_ENV = $VenvDir + +if (-not $Env:VIRTUAL_ENV_DISABLE_PROMPT) { + + Write-Verbose "Setting prompt to '$Prompt'" + + # Set the prompt to include the env name + # Make sure _OLD_VIRTUAL_PROMPT is global + function global:_OLD_VIRTUAL_PROMPT { "" } + Copy-Item -Path function:prompt -Destination function:_OLD_VIRTUAL_PROMPT + New-Variable -Name _PYTHON_VENV_PROMPT_PREFIX -Description "Python virtual environment prompt prefix" -Scope Global -Option ReadOnly -Visibility Public -Value $Prompt + + function global:prompt { + Write-Host -NoNewline -ForegroundColor Green "($_PYTHON_VENV_PROMPT_PREFIX) " + _OLD_VIRTUAL_PROMPT + } +} + +# Clear PYTHONHOME +if (Test-Path -Path Env:PYTHONHOME) { + Copy-Item -Path Env:PYTHONHOME -Destination Env:_OLD_VIRTUAL_PYTHONHOME + Remove-Item -Path Env:PYTHONHOME +} + +# Add the venv to the PATH +Copy-Item -Path Env:PATH -Destination Env:_OLD_VIRTUAL_PATH +$Env:PATH = "$VenvExecDir$([System.IO.Path]::PathSeparator)$Env:PATH" diff --git a/.venv/bin/activate b/.venv/bin/activate new file mode 100644 index 000000000..a703da8f8 --- /dev/null +++ b/.venv/bin/activate @@ -0,0 +1,66 @@ +# This file must be used with "source bin/activate" *from bash* +# you cannot run it directly + +deactivate () { + # reset old environment variables + if [ -n "${_OLD_VIRTUAL_PATH:-}" ] ; then + PATH="${_OLD_VIRTUAL_PATH:-}" + export PATH + unset _OLD_VIRTUAL_PATH + fi + if [ -n "${_OLD_VIRTUAL_PYTHONHOME:-}" ] ; then + PYTHONHOME="${_OLD_VIRTUAL_PYTHONHOME:-}" + export PYTHONHOME + unset _OLD_VIRTUAL_PYTHONHOME + fi + + # This should detect bash and zsh, which have a hash command that must + # be called to get it to forget past commands. Without forgetting + # past commands the $PATH changes we made may not be respected + if [ -n "${BASH:-}" -o -n "${ZSH_VERSION:-}" ] ; then + hash -r 2> /dev/null + fi + + if [ -n "${_OLD_VIRTUAL_PS1:-}" ] ; then + PS1="${_OLD_VIRTUAL_PS1:-}" + export PS1 + unset _OLD_VIRTUAL_PS1 + fi + + unset VIRTUAL_ENV + if [ ! "${1:-}" = "nondestructive" ] ; then + # Self destruct! + unset -f deactivate + fi +} + +# unset irrelevant variables +deactivate nondestructive + +VIRTUAL_ENV="/Users/maxzweig/research/EXOSIMS/.venv" +export VIRTUAL_ENV + +_OLD_VIRTUAL_PATH="$PATH" +PATH="$VIRTUAL_ENV/bin:$PATH" +export PATH + +# unset PYTHONHOME if set +# this will fail if PYTHONHOME is set to the empty string (which is bad anyway) +# could use `if (set -u; : $PYTHONHOME) ;` in bash +if [ -n "${PYTHONHOME:-}" ] ; then + _OLD_VIRTUAL_PYTHONHOME="${PYTHONHOME:-}" + unset PYTHONHOME +fi + +if [ -z "${VIRTUAL_ENV_DISABLE_PROMPT:-}" ] ; then + _OLD_VIRTUAL_PS1="${PS1:-}" + PS1="(.venv) ${PS1:-}" + export PS1 +fi + +# This should detect bash and zsh, which have a hash command that must +# be called to get it to forget past commands. Without forgetting +# past commands the $PATH changes we made may not be respected +if [ -n "${BASH:-}" -o -n "${ZSH_VERSION:-}" ] ; then + hash -r 2> /dev/null +fi diff --git a/.venv/bin/activate.csh b/.venv/bin/activate.csh new file mode 100644 index 000000000..c702ac09f --- /dev/null +++ b/.venv/bin/activate.csh @@ -0,0 +1,25 @@ +# This file must be used with "source bin/activate.csh" *from csh*. +# You cannot run it directly. +# Created by Davide Di Blasi . +# Ported to Python 3.3 venv by Andrew Svetlov + +alias deactivate 'test $?_OLD_VIRTUAL_PATH != 0 && setenv PATH "$_OLD_VIRTUAL_PATH" && unset _OLD_VIRTUAL_PATH; rehash; test $?_OLD_VIRTUAL_PROMPT != 0 && set prompt="$_OLD_VIRTUAL_PROMPT" && unset _OLD_VIRTUAL_PROMPT; unsetenv VIRTUAL_ENV; test "\!:*" != "nondestructive" && unalias deactivate' + +# Unset irrelevant variables. +deactivate nondestructive + +setenv VIRTUAL_ENV "/Users/maxzweig/research/EXOSIMS/.venv" + +set _OLD_VIRTUAL_PATH="$PATH" +setenv PATH "$VIRTUAL_ENV/bin:$PATH" + + +set _OLD_VIRTUAL_PROMPT="$prompt" + +if (! "$?VIRTUAL_ENV_DISABLE_PROMPT") then + set prompt = "(.venv) $prompt" +endif + +alias pydoc python -m pydoc + +rehash diff --git a/.venv/bin/activate.fish b/.venv/bin/activate.fish new file mode 100644 index 000000000..3775ed4ec --- /dev/null +++ b/.venv/bin/activate.fish @@ -0,0 +1,64 @@ +# This file must be used with "source /bin/activate.fish" *from fish* +# (https://fishshell.com/); you cannot run it directly. + +function deactivate -d "Exit virtual environment and return to normal shell environment" + # reset old environment variables + if test -n "$_OLD_VIRTUAL_PATH" + set -gx PATH $_OLD_VIRTUAL_PATH + set -e _OLD_VIRTUAL_PATH + end + if test -n "$_OLD_VIRTUAL_PYTHONHOME" + set -gx PYTHONHOME $_OLD_VIRTUAL_PYTHONHOME + set -e _OLD_VIRTUAL_PYTHONHOME + end + + if test -n "$_OLD_FISH_PROMPT_OVERRIDE" + functions -e fish_prompt + set -e _OLD_FISH_PROMPT_OVERRIDE + functions -c _old_fish_prompt fish_prompt + functions -e _old_fish_prompt + end + + set -e VIRTUAL_ENV + if test "$argv[1]" != "nondestructive" + # Self-destruct! + functions -e deactivate + end +end + +# Unset irrelevant variables. +deactivate nondestructive + +set -gx VIRTUAL_ENV "/Users/maxzweig/research/EXOSIMS/.venv" + +set -gx _OLD_VIRTUAL_PATH $PATH +set -gx PATH "$VIRTUAL_ENV/bin" $PATH + +# Unset PYTHONHOME if set. +if set -q PYTHONHOME + set -gx _OLD_VIRTUAL_PYTHONHOME $PYTHONHOME + set -e PYTHONHOME +end + +if test -z "$VIRTUAL_ENV_DISABLE_PROMPT" + # fish uses a function instead of an env var to generate the prompt. + + # Save the current fish_prompt function as the function _old_fish_prompt. + functions -c fish_prompt _old_fish_prompt + + # With the original prompt function renamed, we can override with our own. + function fish_prompt + # Save the return status of the last command. + set -l old_status $status + + # Output the venv prompt; color taken from the blue of the Python logo. + printf "%s%s%s" (set_color 4B8BBE) "(.venv) " (set_color normal) + + # Restore the return status of the previous command. + echo "exit $old_status" | . + # Output the original/"old" prompt. + _old_fish_prompt + end + + set -gx _OLD_FISH_PROMPT_OVERRIDE "$VIRTUAL_ENV" +end diff --git a/.venv/bin/pip b/.venv/bin/pip new file mode 100755 index 000000000..c0db51a0e --- /dev/null +++ b/.venv/bin/pip @@ -0,0 +1,8 @@ +#!/Users/maxzweig/research/EXOSIMS/.venv/bin/python3 +# -*- coding: utf-8 -*- +import re +import sys +from pip._internal.cli.main import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) diff --git a/.venv/bin/pip3 b/.venv/bin/pip3 new file mode 100755 index 000000000..c0db51a0e --- /dev/null +++ b/.venv/bin/pip3 @@ -0,0 +1,8 @@ +#!/Users/maxzweig/research/EXOSIMS/.venv/bin/python3 +# -*- coding: utf-8 -*- +import re +import sys +from pip._internal.cli.main import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) diff --git a/.venv/bin/pip3.9 b/.venv/bin/pip3.9 new file mode 100755 index 000000000..c0db51a0e --- /dev/null +++ b/.venv/bin/pip3.9 @@ -0,0 +1,8 @@ +#!/Users/maxzweig/research/EXOSIMS/.venv/bin/python3 +# -*- coding: utf-8 -*- +import re +import sys +from pip._internal.cli.main import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) diff --git a/.venv/bin/python b/.venv/bin/python new file mode 120000 index 000000000..b8a0adbbb --- /dev/null +++ b/.venv/bin/python @@ -0,0 +1 @@ +python3 \ No newline at end of file diff --git a/.venv/bin/python3 b/.venv/bin/python3 new file mode 120000 index 000000000..f25545fee --- /dev/null +++ b/.venv/bin/python3 @@ -0,0 +1 @@ +/Library/Developer/CommandLineTools/usr/bin/python3 \ No newline at end of file diff --git a/.venv/bin/python3.9 b/.venv/bin/python3.9 new file mode 120000 index 000000000..b8a0adbbb --- /dev/null +++ b/.venv/bin/python3.9 @@ -0,0 +1 @@ +python3 \ No newline at end of file diff --git a/.venv/pyvenv.cfg b/.venv/pyvenv.cfg new file mode 100644 index 000000000..4760c1ffc --- /dev/null +++ b/.venv/pyvenv.cfg @@ -0,0 +1,3 @@ +home = /Library/Developer/CommandLineTools/usr/bin +include-system-site-packages = false +version = 3.9.6 diff --git a/EXOSIMS/Completeness/GarrettCompleteness.py b/EXOSIMS/Completeness/GarrettCompleteness.py index d42286860..5497c902f 100644 --- a/EXOSIMS/Completeness/GarrettCompleteness.py +++ b/EXOSIMS/Completeness/GarrettCompleteness.py @@ -49,6 +49,9 @@ def __init__(self, order_of_quadrature=15, **specs): self._outspec["order_of_quadrature"] = self.order_of_quadrature + # setting a filename that isn't mutated by a completeness calculation ??? + self.filename_ = self.filename + def completeness_setup(self): """Preform any preliminary calculations needed for this flavor of completeness @@ -206,20 +209,10 @@ def target_completeness(self, TL): int_comp: 1D numpy array of completeness values for each target star """ - - OS = TL.OpticalSystem - if TL.calc_char_int_comp: - mode = list( - filter(lambda mode: "spec" in mode["inst"]["name"], OS.observingModes) - )[0] - else: - mode = list(filter(lambda mode: mode["detectionMode"], OS.observingModes))[ - 0 - ] - # To limit the amount of computation, we want to find the most common # int_dMag value (typically the one the user sets in the input json since # int_dMag is either the user input or the intCutoff_dMag). + vals, counts = np.unique(TL.int_dMag, return_counts=True) self.mode_dMag = vals[np.argwhere(counts == np.max(counts))[0][0]] mode_dMag_mask = TL.int_dMag == self.mode_dMag @@ -234,6 +227,7 @@ def target_completeness(self, TL): ): extstr += "%s: " % att + str(getattr(self.PlanetPopulation, att)) + " " # include mode_dMag and intCutoff_dMag + extstr += ( "%s: " % "mode_dMag" + str(self.mode_dMag) @@ -241,53 +235,111 @@ def target_completeness(self, TL): + " " ) ext = hashlib.md5(extstr.encode("utf-8")).hexdigest() - self.filename += ext - Cpath = os.path.join(self.cachedir, self.filename + ".acomp") - - # calculate separations based on IWA - IWA = mode["IWA"] - OWA = mode["OWA"] - smin = (np.tan(IWA) * TL.dist).to("AU").value - if np.isinf(OWA): - smax = np.array([self.rmax] * len(smin)) - else: - smax = (np.tan(OWA) * TL.dist).to("AU").value - smax[smax > self.rmax] = self.rmax - - int_comp = np.zeros(smin.shape) - # calculate dMags based on maximum dMag - if self.PlanetPopulation.scaleOrbits: - L = np.where(TL.L > 0, TL.L, 1e-10) # take care of zero/negative values - smin = smin / np.sqrt(L) - smax = smax / np.sqrt(L) - dMag_vals = TL.int_dMag - 2.5 * np.log10(L) - separation_mask = smin < self.rmax - int_comp[separation_mask] = self.comp_s( - smin[separation_mask], smax[separation_mask], dMag_vals[separation_mask] - ) + Cpath = os.path.join( + self.cachedir, + self.filename_ + + hashlib.md5("int_comp".encode("utf-8")).hexdigest() + + ext + + ".acomp", + ) + + if os.path.exists(Cpath): + self.vprint('Loading cached int completeness file from "%s".' % Cpath) + try: + with open(Cpath, "rb") as ff: + int_comp = pickle.load(ff) + except UnicodeDecodeError: + with open(Cpath, "rb") as ff: + int_comp = pickle.load(ff, encoding="latin1") + self.vprint("int Completeness loaded from cache.") else: - # In this case we find where the mode dMag value is also in the - # separation range and use the vectorized integral since they have - # the same dMag value. Where the dMag values are not the mode we - # must use comp_s which is slower - dMag_vals = TL.int_dMag - separation_mask = smin < self.rmax - dist_s = self.genComp(Cpath, TL) - dist_sv = np.vectorize(dist_s.integral, otypes=[np.float64]) - separation_mode_mask = separation_mask & mode_dMag_mask - separation_not_mode_mask = separation_mask & ~mode_dMag_mask - int_comp[separation_mode_mask] = dist_sv( - smin[separation_mode_mask], smax[separation_mode_mask] - ) - int_comp[separation_not_mode_mask] = self.comp_s( - smin[separation_not_mode_mask], - smax[separation_not_mode_mask], - dMag_vals[separation_not_mode_mask], + + self.vprint('Cached int completeness file not found at "%s".' % Cpath) + self.vprint("Beginning int_comp completeness calculations.") + + OS = TL.OpticalSystem + if TL.calc_char_int_comp: + mode = list( + filter( + lambda mode: "spec" in mode["inst"]["name"], OS.observingModes + ) + )[0] + else: + mode = list( + filter(lambda mode: mode["detectionMode"], OS.observingModes) + )[0] + + # important PlanetPopulation attributes + atts = list(self.PlanetPopulation.__dict__) + extstr = "" + for att in sorted(atts, key=str.lower): + if ( + not callable(getattr(self.PlanetPopulation, att)) + and att != "PlanetPhysicalModel" + ): + extstr += ( + "%s: " % att + str(getattr(self.PlanetPopulation, att)) + " " + ) + # include mode_dMag and intCutoff_dMag + extstr += ( + "%s: " % "mode_dMag" + + str(self.mode_dMag) + + f"intCutoff_dMag: {TL.intCutoff_dMag}" + + " " ) - # ensure that completeness values are between 0 and 1 - int_comp = np.clip(int_comp, 0.0, 1.0) + ext = hashlib.md5(extstr.encode("utf-8")).hexdigest() + Cpath_aux = os.path.join(self.cachedir, self.filename_ + ext + ".acomp") + self.filename += ext + + # calculate separations based on IWA + IWA = mode["IWA"] + OWA = mode["OWA"] + smin = (np.tan(IWA) * TL.dist).to("AU").value + if np.isinf(OWA): + smax = np.array([self.rmax] * len(smin)) + else: + smax = (np.tan(OWA) * TL.dist).to("AU").value + smax[smax > self.rmax] = self.rmax + + int_comp = np.zeros(smin.shape) + # calculate dMags based on maximum dMag + if self.PlanetPopulation.scaleOrbits: + L = np.where(TL.L > 0, TL.L, 1e-10) # take care of zero/negative values + smin = smin / np.sqrt(L) + smax = smax / np.sqrt(L) + dMag_vals = TL.int_dMag - 2.5 * np.log10(L) + separation_mask = smin < self.rmax + int_comp[separation_mask] = self.comp_s( + smin[separation_mask], + smax[separation_mask], + dMag_vals[separation_mask], + ) + else: + # In this case we find where the mode dMag value is also in the + # separation range and use the vectorized integral since they have + # the same dMag value. Where the dMag values are not the mode we + # must use comp_s which is slower + dMag_vals = TL.int_dMag + separation_mask = smin < self.rmax + dist_s = self.genComp(Cpath_aux, TL) + dist_sv = np.vectorize(dist_s.integral, otypes=[np.float64]) + separation_mode_mask = separation_mask & mode_dMag_mask + separation_not_mode_mask = separation_mask & ~mode_dMag_mask + int_comp[separation_mode_mask] = dist_sv( + smin[separation_mode_mask], smax[separation_mode_mask] + ) + int_comp[separation_not_mode_mask] = self.comp_s( + smin[separation_not_mode_mask], + smax[separation_not_mode_mask], + dMag_vals[separation_not_mode_mask], + ) + # ensure that completeness values are between 0 and 1 + int_comp = np.clip(int_comp, 0.0, 1.0) + with open(Cpath, "wb") as ff: + pickle.dump(int_comp, ff) + self.vprint("Int Completeness data stored in %s" % Cpath) return int_comp def genComp(self, Cpath, TL): @@ -308,7 +360,7 @@ def genComp(self, Cpath, TL): if os.path.exists(Cpath): # dist_s interpolant already exists for parameters - self.vprint("Loading cached completeness file from %s" % Cpath) + self.vprint("Loading cached completeness pdf file from %s" % Cpath) try: with open(Cpath, "rb") as ff: H = pickle.load(ff) @@ -334,7 +386,7 @@ def genComp(self, Cpath, TL): H = {"dist_s": dist_s} with open(Cpath, "wb") as ff: pickle.dump(H, ff) - self.vprint("Completeness data stored in %s" % Cpath) + self.vprint("Completeness pdf data stored in %s" % Cpath) return dist_s diff --git a/test-reports/TEST-tests.BackgroundSources.test_BackgroundSources.TestBackgroundSources-20240612212837.xml b/test-reports/TEST-tests.BackgroundSources.test_BackgroundSources.TestBackgroundSources-20240612212837.xml new file mode 100644 index 000000000..6e1983722 --- /dev/null +++ b/test-reports/TEST-tests.BackgroundSources.test_BackgroundSources.TestBackgroundSources-20240612212837.xml @@ -0,0 +1,11 @@ + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613191607.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613191607.xml new file mode 100644 index 000000000..08d80ddaf --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613191607.xml @@ -0,0 +1,11 @@ + + + + + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613191619.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613191619.xml new file mode 100644 index 000000000..1ff6ed3aa --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613191619.xml @@ -0,0 +1,11 @@ + + + + + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613192133.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613192133.xml new file mode 100644 index 000000000..3ea80acd6 --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613192133.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613192645.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613192645.xml new file mode 100644 index 000000000..34bc92ac3 --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613192645.xml @@ -0,0 +1,45 @@ + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613192747.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613192747.xml new file mode 100644 index 000000000..783dc2439 --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613192747.xml @@ -0,0 +1,45 @@ + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613192910.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613192910.xml new file mode 100644 index 000000000..69684eff5 --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613192910.xml @@ -0,0 +1,45 @@ + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613193030.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613193030.xml new file mode 100644 index 000000000..36c5fe05d --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613193030.xml @@ -0,0 +1,45 @@ + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613194151.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613194151.xml new file mode 100644 index 000000000..f1dd07afb --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613194151.xml @@ -0,0 +1,96 @@ + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613194254.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613194254.xml new file mode 100644 index 000000000..99a3a19e2 --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613194254.xml @@ -0,0 +1,96 @@ + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613194902.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613194902.xml new file mode 100644 index 000000000..ff4dd3ffb --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613194902.xml @@ -0,0 +1,96 @@ + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613194956.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613194956.xml new file mode 100644 index 000000000..b5d855139 --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613194956.xml @@ -0,0 +1,96 @@ + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613195056.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613195056.xml new file mode 100644 index 000000000..8cc26ba6e --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613195056.xml @@ -0,0 +1,96 @@ + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613195130.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613195130.xml new file mode 100644 index 000000000..4c7c0cb5c --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613195130.xml @@ -0,0 +1,96 @@ + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613195502.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613195502.xml new file mode 100644 index 000000000..5daac4478 --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613195502.xml @@ -0,0 +1,45 @@ + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613195521.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613195521.xml new file mode 100644 index 000000000..d8d1e5e65 --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613195521.xml @@ -0,0 +1,45 @@ + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613202943.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613202943.xml new file mode 100644 index 000000000..6614a958b --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613202943.xml @@ -0,0 +1,45 @@ + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613203005.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613203005.xml new file mode 100644 index 000000000..da1f46e95 --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613203005.xml @@ -0,0 +1,45 @@ + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613203241.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613203241.xml new file mode 100644 index 000000000..409557002 --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613203241.xml @@ -0,0 +1,30 @@ + + + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613203854.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613203854.xml new file mode 100644 index 000000000..1b2486ad1 --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613203854.xml @@ -0,0 +1,32 @@ + + + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613203916.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613203916.xml new file mode 100644 index 000000000..51f05e6be --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613203916.xml @@ -0,0 +1,32 @@ + + + + + + + + + diff --git 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--git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613222533.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613222533.xml new file mode 100644 index 000000000..f163f5ebe --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613222533.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613222702.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613222702.xml new file mode 100644 index 000000000..d0df5bd36 --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613222702.xml @@ -0,0 +1,49 @@ + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613222850.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613222850.xml new file mode 100644 index 000000000..fb64096ea --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613222850.xml @@ -0,0 +1,37 @@ + + + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613222938.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613222938.xml new file mode 100644 index 000000000..798bddf42 --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613222938.xml @@ -0,0 +1,37 @@ + + + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613223001.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613223001.xml new file mode 100644 index 000000000..61237eef0 --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613223001.xml @@ -0,0 +1,54 @@ + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613223330.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613223330.xml new file mode 100644 index 000000000..e03d96294 --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613223330.xml @@ -0,0 +1,11 @@ + + + + + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613223346.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613223346.xml new file mode 100644 index 000000000..4bd69d136 --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613223346.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613223405.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613223405.xml new file mode 100644 index 000000000..110b59223 --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613223405.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613223429.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613223429.xml new file mode 100644 index 000000000..33997de2b --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613223429.xml @@ -0,0 +1,122 @@ + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613223517.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613223517.xml new file mode 100644 index 000000000..5e56f497d --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240613223517.xml @@ -0,0 +1,47 @@ + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240614220203.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240614220203.xml new file mode 100644 index 000000000..c10834f8e --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240614220203.xml @@ -0,0 +1,47 @@ + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240614231320.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240614231320.xml new file mode 100644 index 000000000..c2bb896e6 --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240614231320.xml @@ -0,0 +1,57 @@ + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240614231935.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240614231935.xml new file mode 100644 index 000000000..b547b950e --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240614231935.xml @@ -0,0 +1,47 @@ + + + + + + + diff --git a/test-reports/TEST-unittest.loader._FailedTest-20240612212614.xml b/test-reports/TEST-unittest.loader._FailedTest-20240612212614.xml new file mode 100644 index 000000000..dd5b2e49d --- /dev/null +++ b/test-reports/TEST-unittest.loader._FailedTest-20240612212614.xml @@ -0,0 +1,19 @@ + + + + + + + + diff --git a/test-reports/TEST-unittest.loader._FailedTest-20240613191413.xml b/test-reports/TEST-unittest.loader._FailedTest-20240613191413.xml new file mode 100644 index 000000000..baa97ba17 --- /dev/null +++ b/test-reports/TEST-unittest.loader._FailedTest-20240613191413.xml @@ -0,0 +1,19 @@ + + + + + + + + diff --git a/test-reports/TEST-unittest.loader._FailedTest-20240613191513.xml b/test-reports/TEST-unittest.loader._FailedTest-20240613191513.xml new file mode 100644 index 000000000..4ea38497d --- /dev/null +++ b/test-reports/TEST-unittest.loader._FailedTest-20240613191513.xml @@ -0,0 +1,19 @@ + + + + + + + + diff --git a/test-reports/TEST-unittest.loader._FailedTest-20240613191534.xml b/test-reports/TEST-unittest.loader._FailedTest-20240613191534.xml new file mode 100644 index 000000000..a6565d9a3 --- /dev/null +++ b/test-reports/TEST-unittest.loader._FailedTest-20240613191534.xml @@ -0,0 +1,19 @@ + + + + + + + + diff --git a/tests/Completeness/test_BrownvGarrett.py b/tests/Completeness/test_BrownvGarrett.py index 99c9cc844..cf7c4cf35 100644 --- a/tests/Completeness/test_BrownvGarrett.py +++ b/tests/Completeness/test_BrownvGarrett.py @@ -27,7 +27,7 @@ def setUp(self): with open(self.script) as f: self.spec = json.loads(f.read()) - @unittest.skip("Skipping Garrett vs Brown comparison tests.") + # @unittest.skip("Skipping Garrett vs Brown comparison tests.") def test_target_completeness_def(self): """ Compare calculated completenesses for multiple targets under default population @@ -64,6 +64,7 @@ def test_target_completeness_def(self): cBrown = Brown.target_completeness(TL) cGarrett = Garrett.target_completeness(TL) + cGarrett = Garrett.target_completeness(TL) np.testing.assert_allclose(cGarrett, cBrown, rtol=0.1, atol=1e-6) @@ -83,7 +84,7 @@ def test_target_completeness_def(self): self.assertLessEqual(meandiff, 0.1) - @unittest.skip("Skipping Garrett vs Brown comparison tests.") + # @unittest.skip("Skipping Garrett vs Brown comparison tests.") def test_target_completeness_constrainOrbits(self): """ Compare calculated completenesses for multiple targets with constrain orbits set to true From 3bfba44337c3c7f5addbd4d98bd773a9945b6d4c Mon Sep 17 00:00:00 2001 From: Maxwlel Date: Sun, 16 Jun 2024 11:43:44 -0400 Subject: [PATCH 2/6] cache target completeness fix --- ...rrett.TestBrownvGarrett-20240616113238.xml | 11 +++++ ...rrett.TestBrownvGarrett-20240616113252.xml | 45 +++++++++++++++++++ tests/Completeness/test_BrownvGarrett.py | 3 +- 3 files changed, 57 insertions(+), 2 deletions(-) create mode 100644 test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240616113238.xml create mode 100644 test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240616113252.xml diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240616113238.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240616113238.xml new file mode 100644 index 000000000..c1fb2809e --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240616113238.xml @@ -0,0 +1,11 @@ + + + + + + + + + + + diff --git a/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240616113252.xml b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240616113252.xml new file mode 100644 index 000000000..9b322a641 --- /dev/null +++ b/test-reports/TEST-tests.Completeness.test_BrownvGarrett.TestBrownvGarrett-20240616113252.xml @@ -0,0 +1,45 @@ + + + + + + + diff --git a/tests/Completeness/test_BrownvGarrett.py b/tests/Completeness/test_BrownvGarrett.py index cf7c4cf35..af8cf0a19 100644 --- a/tests/Completeness/test_BrownvGarrett.py +++ b/tests/Completeness/test_BrownvGarrett.py @@ -64,7 +64,6 @@ def test_target_completeness_def(self): cBrown = Brown.target_completeness(TL) cGarrett = Garrett.target_completeness(TL) - cGarrett = Garrett.target_completeness(TL) np.testing.assert_allclose(cGarrett, cBrown, rtol=0.1, atol=1e-6) @@ -84,7 +83,7 @@ def test_target_completeness_def(self): self.assertLessEqual(meandiff, 0.1) - # @unittest.skip("Skipping Garrett vs Brown comparison tests.") + # @unittest.skip("Skipping Garrett vs Brown comparison tests.") def test_target_completeness_constrainOrbits(self): """ Compare calculated completenesses for multiple targets with constrain orbits set to true From 2edf47b24a5f9e2108527fbaabbd39fa56535a03 Mon Sep 17 00:00:00 2001 From: Maxwlel Date: Sun, 16 Jun 2024 13:38:37 -0400 Subject: [PATCH 3/6] blackening code --- .venv/bin/Activate.ps1 | 241 ----------------------- .venv/bin/activate | 66 ------- .venv/bin/activate.csh | 25 --- .venv/bin/activate.fish | 64 ------ .venv/bin/pip | 8 - .venv/bin/pip3 | 8 - .venv/bin/pip3.9 | 8 - .venv/bin/python | 1 - .venv/bin/python3 | 1 - .venv/bin/python3.9 | 1 - .venv/pyvenv.cfg | 3 - documentation/conf.py | 209 ++++++++++---------- tests/Completeness/test_BrownvGarrett.py | 4 +- tools/evenlyDistributePointsOnSphere.py | 8 +- tools/gen_spectral_library_index.py | 2 +- 15 files changed, 111 insertions(+), 538 deletions(-) delete mode 100644 .venv/bin/Activate.ps1 delete mode 100644 .venv/bin/activate delete mode 100644 .venv/bin/activate.csh delete mode 100644 .venv/bin/activate.fish delete mode 100755 .venv/bin/pip delete mode 100755 .venv/bin/pip3 delete mode 100755 .venv/bin/pip3.9 delete mode 120000 .venv/bin/python delete mode 120000 .venv/bin/python3 delete mode 120000 .venv/bin/python3.9 delete mode 100644 .venv/pyvenv.cfg diff --git a/.venv/bin/Activate.ps1 b/.venv/bin/Activate.ps1 deleted file mode 100644 index 2fb3852c3..000000000 --- a/.venv/bin/Activate.ps1 +++ /dev/null @@ -1,241 +0,0 @@ -<# -.Synopsis -Activate a Python virtual environment for the current PowerShell session. - -.Description -Pushes the python executable for a virtual environment to the front of the -$Env:PATH environment variable and sets the prompt to signify that you are -in a Python virtual environment. Makes use of the command line switches as -well as the `pyvenv.cfg` file values present in the virtual environment. - -.Parameter VenvDir -Path to the directory that contains the virtual environment to activate. The -default value for this is the parent of the directory that the Activate.ps1 -script is located within. - -.Parameter Prompt -The prompt prefix to display when this virtual environment is activated. By -default, this prompt is the name of the virtual environment folder (VenvDir) -surrounded by parentheses and followed by a single space (ie. '(.venv) '). - -.Example -Activate.ps1 -Activates the Python virtual environment that contains the Activate.ps1 script. - -.Example -Activate.ps1 -Verbose -Activates the Python virtual environment that contains the Activate.ps1 script, -and shows extra information about the activation as it executes. - -.Example -Activate.ps1 -VenvDir C:\Users\MyUser\Common\.venv -Activates the Python virtual environment located in the specified location. - -.Example -Activate.ps1 -Prompt "MyPython" -Activates the Python virtual environment that contains the Activate.ps1 script, -and prefixes the current prompt with the specified string (surrounded in -parentheses) while the virtual environment is active. - -.Notes -On Windows, it may be required to enable this Activate.ps1 script by setting the -execution policy for the user. You can do this by issuing the following PowerShell -command: - -PS C:\> Set-ExecutionPolicy -ExecutionPolicy RemoteSigned -Scope CurrentUser - -For more information on Execution Policies: -https://go.microsoft.com/fwlink/?LinkID=135170 - -#> -Param( - [Parameter(Mandatory = $false)] - [String] - $VenvDir, - [Parameter(Mandatory = $false)] - [String] - $Prompt -) - -<# Function declarations --------------------------------------------------- #> - -<# -.Synopsis -Remove all shell session elements added by the Activate script, including the -addition of the virtual environment's Python executable from the beginning of -the PATH variable. - -.Parameter NonDestructive -If present, do not remove this function from the global namespace for the -session. - -#> -function global:deactivate ([switch]$NonDestructive) { - # Revert to original values - - # The prior prompt: - if (Test-Path -Path Function:_OLD_VIRTUAL_PROMPT) { - Copy-Item -Path Function:_OLD_VIRTUAL_PROMPT -Destination Function:prompt - Remove-Item -Path Function:_OLD_VIRTUAL_PROMPT - } - - # The prior PYTHONHOME: - if (Test-Path -Path Env:_OLD_VIRTUAL_PYTHONHOME) { - Copy-Item -Path Env:_OLD_VIRTUAL_PYTHONHOME -Destination Env:PYTHONHOME - Remove-Item -Path Env:_OLD_VIRTUAL_PYTHONHOME - } - - # The prior PATH: - if (Test-Path -Path Env:_OLD_VIRTUAL_PATH) { - Copy-Item -Path Env:_OLD_VIRTUAL_PATH -Destination Env:PATH - Remove-Item -Path Env:_OLD_VIRTUAL_PATH - } - - # Just remove the VIRTUAL_ENV altogether: - if (Test-Path -Path Env:VIRTUAL_ENV) { - Remove-Item -Path env:VIRTUAL_ENV - } - - # Just remove the _PYTHON_VENV_PROMPT_PREFIX altogether: - if (Get-Variable -Name "_PYTHON_VENV_PROMPT_PREFIX" -ErrorAction SilentlyContinue) { - Remove-Variable -Name _PYTHON_VENV_PROMPT_PREFIX -Scope Global -Force - } - - # Leave deactivate function in the global namespace if requested: - if (-not $NonDestructive) { - Remove-Item -Path function:deactivate - } -} - -<# -.Description -Get-PyVenvConfig parses the values from the pyvenv.cfg file located in the -given folder, and returns them in a map. - -For each line in the pyvenv.cfg file, if that line can be parsed into exactly -two strings separated by `=` (with any amount of whitespace surrounding the =) -then it is considered a `key = value` line. The left hand string is the key, -the right hand is the value. - -If the value starts with a `'` or a `"` then the first and last character is -stripped from the value before being captured. - -.Parameter ConfigDir -Path to the directory that contains the `pyvenv.cfg` file. -#> -function Get-PyVenvConfig( - [String] - $ConfigDir -) { - Write-Verbose "Given ConfigDir=$ConfigDir, obtain values in pyvenv.cfg" - - # Ensure the file exists, and issue a warning if it doesn't (but still allow the function to continue). - $pyvenvConfigPath = Join-Path -Resolve -Path $ConfigDir -ChildPath 'pyvenv.cfg' -ErrorAction Continue - - # An empty map will be returned if no config file is found. - $pyvenvConfig = @{ } - - if ($pyvenvConfigPath) { - - Write-Verbose "File exists, parse `key = value` lines" - $pyvenvConfigContent = Get-Content -Path $pyvenvConfigPath - - $pyvenvConfigContent | ForEach-Object { - $keyval = $PSItem -split "\s*=\s*", 2 - if ($keyval[0] -and $keyval[1]) { - $val = $keyval[1] - - # Remove extraneous quotations around a string value. - if ("'""".Contains($val.Substring(0, 1))) { - $val = $val.Substring(1, $val.Length - 2) - } - - $pyvenvConfig[$keyval[0]] = $val - Write-Verbose "Adding Key: '$($keyval[0])'='$val'" - } - } - } - return $pyvenvConfig -} - - -<# Begin Activate script --------------------------------------------------- #> - -# Determine the containing directory of this script -$VenvExecPath = Split-Path -Parent $MyInvocation.MyCommand.Definition -$VenvExecDir = Get-Item -Path $VenvExecPath - -Write-Verbose "Activation script is located in path: '$VenvExecPath'" -Write-Verbose "VenvExecDir Fullname: '$($VenvExecDir.FullName)" -Write-Verbose "VenvExecDir Name: '$($VenvExecDir.Name)" - -# Set values required in priority: CmdLine, ConfigFile, Default -# First, get the location of the virtual environment, it might not be -# VenvExecDir if specified on the command line. -if ($VenvDir) { - Write-Verbose "VenvDir given as parameter, using '$VenvDir' to determine values" -} -else { - Write-Verbose "VenvDir not given as a parameter, using parent directory name as VenvDir." - $VenvDir = $VenvExecDir.Parent.FullName.TrimEnd("\\/") - Write-Verbose "VenvDir=$VenvDir" -} - -# Next, read the `pyvenv.cfg` file to determine any required value such -# as `prompt`. -$pyvenvCfg = Get-PyVenvConfig -ConfigDir $VenvDir - -# Next, set the prompt from the command line, or the config file, or -# just use the name of the virtual environment folder. -if ($Prompt) { - Write-Verbose "Prompt specified as argument, using '$Prompt'" -} -else { - Write-Verbose "Prompt not specified as argument to script, checking pyvenv.cfg value" - if ($pyvenvCfg -and $pyvenvCfg['prompt']) { - Write-Verbose " Setting based on value in pyvenv.cfg='$($pyvenvCfg['prompt'])'" - $Prompt = $pyvenvCfg['prompt']; - } - else { - Write-Verbose " Setting prompt based on parent's directory's name. (Is the directory name passed to venv module when creating the virutal environment)" - Write-Verbose " Got leaf-name of $VenvDir='$(Split-Path -Path $venvDir -Leaf)'" - $Prompt = Split-Path -Path $venvDir -Leaf - } -} - -Write-Verbose "Prompt = '$Prompt'" -Write-Verbose "VenvDir='$VenvDir'" - -# Deactivate any currently active virtual environment, but leave the -# deactivate function in place. -deactivate -nondestructive - -# Now set the environment variable VIRTUAL_ENV, used by many tools to determine -# that there is an activated venv. -$env:VIRTUAL_ENV = $VenvDir - -if (-not $Env:VIRTUAL_ENV_DISABLE_PROMPT) { - - Write-Verbose "Setting prompt to '$Prompt'" - - # Set the prompt to include the env name - # Make sure _OLD_VIRTUAL_PROMPT is global - function global:_OLD_VIRTUAL_PROMPT { "" } - Copy-Item -Path function:prompt -Destination function:_OLD_VIRTUAL_PROMPT - New-Variable -Name _PYTHON_VENV_PROMPT_PREFIX -Description "Python virtual environment prompt prefix" -Scope Global -Option ReadOnly -Visibility Public -Value $Prompt - - function global:prompt { - Write-Host -NoNewline -ForegroundColor Green "($_PYTHON_VENV_PROMPT_PREFIX) " - _OLD_VIRTUAL_PROMPT - } -} - -# Clear PYTHONHOME -if (Test-Path -Path Env:PYTHONHOME) { - Copy-Item -Path Env:PYTHONHOME -Destination Env:_OLD_VIRTUAL_PYTHONHOME - Remove-Item -Path Env:PYTHONHOME -} - -# Add the venv to the PATH -Copy-Item -Path Env:PATH -Destination Env:_OLD_VIRTUAL_PATH -$Env:PATH = "$VenvExecDir$([System.IO.Path]::PathSeparator)$Env:PATH" diff --git a/.venv/bin/activate b/.venv/bin/activate deleted file mode 100644 index a703da8f8..000000000 --- a/.venv/bin/activate +++ /dev/null @@ -1,66 +0,0 @@ -# This file must be used with "source bin/activate" *from bash* -# you cannot run it directly - -deactivate () { - # reset old environment variables - if [ -n "${_OLD_VIRTUAL_PATH:-}" ] ; then - PATH="${_OLD_VIRTUAL_PATH:-}" - export PATH - unset _OLD_VIRTUAL_PATH - fi - if [ -n "${_OLD_VIRTUAL_PYTHONHOME:-}" ] ; then - PYTHONHOME="${_OLD_VIRTUAL_PYTHONHOME:-}" - export PYTHONHOME - unset _OLD_VIRTUAL_PYTHONHOME - fi - - # This should detect bash and zsh, which have a hash command that must - # be called to get it to forget past commands. Without forgetting - # past commands the $PATH changes we made may not be respected - if [ -n "${BASH:-}" -o -n "${ZSH_VERSION:-}" ] ; then - hash -r 2> /dev/null - fi - - if [ -n "${_OLD_VIRTUAL_PS1:-}" ] ; then - PS1="${_OLD_VIRTUAL_PS1:-}" - export PS1 - unset _OLD_VIRTUAL_PS1 - fi - - unset VIRTUAL_ENV - if [ ! "${1:-}" = "nondestructive" ] ; then - # Self destruct! - unset -f deactivate - fi -} - -# unset irrelevant variables -deactivate nondestructive - -VIRTUAL_ENV="/Users/maxzweig/research/EXOSIMS/.venv" -export VIRTUAL_ENV - -_OLD_VIRTUAL_PATH="$PATH" -PATH="$VIRTUAL_ENV/bin:$PATH" -export PATH - -# unset PYTHONHOME if set -# this will fail if PYTHONHOME is set to the empty string (which is bad anyway) -# could use `if (set -u; : $PYTHONHOME) ;` in bash -if [ -n "${PYTHONHOME:-}" ] ; then - _OLD_VIRTUAL_PYTHONHOME="${PYTHONHOME:-}" - unset PYTHONHOME -fi - -if [ -z "${VIRTUAL_ENV_DISABLE_PROMPT:-}" ] ; then - _OLD_VIRTUAL_PS1="${PS1:-}" - PS1="(.venv) ${PS1:-}" - export PS1 -fi - -# This should detect bash and zsh, which have a hash command that must -# be called to get it to forget past commands. Without forgetting -# past commands the $PATH changes we made may not be respected -if [ -n "${BASH:-}" -o -n "${ZSH_VERSION:-}" ] ; then - hash -r 2> /dev/null -fi diff --git a/.venv/bin/activate.csh b/.venv/bin/activate.csh deleted file mode 100644 index c702ac09f..000000000 --- a/.venv/bin/activate.csh +++ /dev/null @@ -1,25 +0,0 @@ -# This file must be used with "source bin/activate.csh" *from csh*. -# You cannot run it directly. -# Created by Davide Di Blasi . -# Ported to Python 3.3 venv by Andrew Svetlov - -alias deactivate 'test $?_OLD_VIRTUAL_PATH != 0 && setenv PATH "$_OLD_VIRTUAL_PATH" && unset _OLD_VIRTUAL_PATH; rehash; test $?_OLD_VIRTUAL_PROMPT != 0 && set prompt="$_OLD_VIRTUAL_PROMPT" && unset _OLD_VIRTUAL_PROMPT; unsetenv VIRTUAL_ENV; test "\!:*" != "nondestructive" && unalias deactivate' - -# Unset irrelevant variables. -deactivate nondestructive - -setenv VIRTUAL_ENV "/Users/maxzweig/research/EXOSIMS/.venv" - -set _OLD_VIRTUAL_PATH="$PATH" -setenv PATH "$VIRTUAL_ENV/bin:$PATH" - - -set _OLD_VIRTUAL_PROMPT="$prompt" - -if (! "$?VIRTUAL_ENV_DISABLE_PROMPT") then - set prompt = "(.venv) $prompt" -endif - -alias pydoc python -m pydoc - -rehash diff --git a/.venv/bin/activate.fish b/.venv/bin/activate.fish deleted file mode 100644 index 3775ed4ec..000000000 --- a/.venv/bin/activate.fish +++ /dev/null @@ -1,64 +0,0 @@ -# This file must be used with "source /bin/activate.fish" *from fish* -# (https://fishshell.com/); you cannot run it directly. - -function deactivate -d "Exit virtual environment and return to normal shell environment" - # reset old environment variables - if test -n "$_OLD_VIRTUAL_PATH" - set -gx PATH $_OLD_VIRTUAL_PATH - set -e _OLD_VIRTUAL_PATH - end - if test -n "$_OLD_VIRTUAL_PYTHONHOME" - set -gx PYTHONHOME $_OLD_VIRTUAL_PYTHONHOME - set -e _OLD_VIRTUAL_PYTHONHOME - end - - if test -n "$_OLD_FISH_PROMPT_OVERRIDE" - functions -e fish_prompt - set -e _OLD_FISH_PROMPT_OVERRIDE - functions -c _old_fish_prompt fish_prompt - functions -e _old_fish_prompt - end - - set -e VIRTUAL_ENV - if test "$argv[1]" != "nondestructive" - # Self-destruct! - functions -e deactivate - end -end - -# Unset irrelevant variables. -deactivate nondestructive - -set -gx VIRTUAL_ENV "/Users/maxzweig/research/EXOSIMS/.venv" - -set -gx _OLD_VIRTUAL_PATH $PATH -set -gx PATH "$VIRTUAL_ENV/bin" $PATH - -# Unset PYTHONHOME if set. -if set -q PYTHONHOME - set -gx _OLD_VIRTUAL_PYTHONHOME $PYTHONHOME - set -e PYTHONHOME -end - -if test -z "$VIRTUAL_ENV_DISABLE_PROMPT" - # fish uses a function instead of an env var to generate the prompt. - - # Save the current fish_prompt function as the function _old_fish_prompt. - functions -c fish_prompt _old_fish_prompt - - # With the original prompt function renamed, we can override with our own. - function fish_prompt - # Save the return status of the last command. - set -l old_status $status - - # Output the venv prompt; color taken from the blue of the Python logo. - printf "%s%s%s" (set_color 4B8BBE) "(.venv) " (set_color normal) - - # Restore the return status of the previous command. - echo "exit $old_status" | . - # Output the original/"old" prompt. - _old_fish_prompt - end - - set -gx _OLD_FISH_PROMPT_OVERRIDE "$VIRTUAL_ENV" -end diff --git a/.venv/bin/pip b/.venv/bin/pip deleted file mode 100755 index c0db51a0e..000000000 --- a/.venv/bin/pip +++ /dev/null @@ -1,8 +0,0 @@ -#!/Users/maxzweig/research/EXOSIMS/.venv/bin/python3 -# -*- coding: utf-8 -*- -import re -import sys -from pip._internal.cli.main import main -if __name__ == '__main__': - sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) - sys.exit(main()) diff --git a/.venv/bin/pip3 b/.venv/bin/pip3 deleted file mode 100755 index c0db51a0e..000000000 --- a/.venv/bin/pip3 +++ /dev/null @@ -1,8 +0,0 @@ -#!/Users/maxzweig/research/EXOSIMS/.venv/bin/python3 -# -*- coding: utf-8 -*- -import re -import sys -from pip._internal.cli.main import main -if __name__ == '__main__': - sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) - sys.exit(main()) diff --git a/.venv/bin/pip3.9 b/.venv/bin/pip3.9 deleted file mode 100755 index c0db51a0e..000000000 --- a/.venv/bin/pip3.9 +++ /dev/null @@ -1,8 +0,0 @@ -#!/Users/maxzweig/research/EXOSIMS/.venv/bin/python3 -# -*- coding: utf-8 -*- -import re -import sys -from pip._internal.cli.main import main -if __name__ == '__main__': - sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) - sys.exit(main()) diff --git a/.venv/bin/python b/.venv/bin/python deleted file mode 120000 index b8a0adbbb..000000000 --- a/.venv/bin/python +++ /dev/null @@ -1 +0,0 @@ -python3 \ No newline at end of file diff --git a/.venv/bin/python3 b/.venv/bin/python3 deleted file mode 120000 index f25545fee..000000000 --- a/.venv/bin/python3 +++ /dev/null @@ -1 +0,0 @@ -/Library/Developer/CommandLineTools/usr/bin/python3 \ No newline at end of file diff --git a/.venv/bin/python3.9 b/.venv/bin/python3.9 deleted file mode 120000 index b8a0adbbb..000000000 --- a/.venv/bin/python3.9 +++ /dev/null @@ -1 +0,0 @@ -python3 \ No newline at end of file diff --git a/.venv/pyvenv.cfg b/.venv/pyvenv.cfg deleted file mode 100644 index 4760c1ffc..000000000 --- a/.venv/pyvenv.cfg +++ /dev/null @@ -1,3 +0,0 @@ -home = /Library/Developer/CommandLineTools/usr/bin -include-system-site-packages = false -version = 3.9.6 diff --git a/documentation/conf.py b/documentation/conf.py index 10a6e0336..af4f4bff8 100644 --- a/documentation/conf.py +++ b/documentation/conf.py @@ -19,56 +19,56 @@ # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. -#sys.path.insert(0, os.path.abspath('.')) -sys.path.insert(0, os.path.abspath('..')) +# sys.path.insert(0, os.path.abspath('.')) +sys.path.insert(0, os.path.abspath("..")) # -- General configuration ------------------------------------------------ # If your documentation needs a minimal Sphinx version, state it here. -#needs_sphinx = '1.0' +# needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ - 'sphinx.ext.autodoc', - 'sphinx.ext.napoleon', - 'sphinx.ext.todo', - 'sphinx.ext.coverage', - 'sphinx.ext.mathjax', - 'sphinx.ext.ifconfig', - 'sphinx.ext.viewcode', - 'sphinx.ext.intersphinx', - 'sphinxcontrib.mermaid' + "sphinx.ext.autodoc", + "sphinx.ext.napoleon", + "sphinx.ext.todo", + "sphinx.ext.coverage", + "sphinx.ext.mathjax", + "sphinx.ext.ifconfig", + "sphinx.ext.viewcode", + "sphinx.ext.intersphinx", + "sphinxcontrib.mermaid", ] # Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] +templates_path = ["_templates"] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # source_suffix = ['.rst', '.md'] -source_suffix = '.rst' +source_suffix = ".rst" # The encoding of source files. -#source_encoding = 'utf-8-sig' +# source_encoding = 'utf-8-sig' # The master toctree document. -master_doc = 'index' +master_doc = "index" # General information about the project. -project = u'EXOSIMS' -copyright = u'2015 - 2023, SIOSlab' -author = u'SIOSlab' +project = "EXOSIMS" +copyright = "2015 - 2023, SIOSlab" +author = "SIOSlab" # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. -#version = '2.1' +# version = '2.1' # The full version, including alpha/beta/rc tags. -#release = '2.1.0' +# release = '2.1.0' with open(os.path.join("..", "EXOSIMS", "__init__.py"), "r") as f: version_file = f.read() @@ -86,41 +86,41 @@ # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. -#language = None +# language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: -#today = '' +# today = '' # Else, today_fmt is used as the format for a strftime call. -#today_fmt = '%B %d, %Y' +# today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. -exclude_patterns = ['_build', '.DS_Store'] +exclude_patterns = ["_build", ".DS_Store"] # The reST default role (used for this markup: `text`) to use for all # documents. -#default_role = None +# default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. -#add_function_parentheses = True +# add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). -#add_module_names = True +# add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. -#show_authors = False +# show_authors = False # The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' +pygments_style = "sphinx" # A list of ignored prefixes for module index sorting. -#modindex_common_prefix = [] +# modindex_common_prefix = [] # If true, keep warnings as "system message" paragraphs in the built documents. -#keep_warnings = False +# keep_warnings = False # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = True @@ -130,164 +130,157 @@ # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. -#html_theme = 'alabaster' +# html_theme = 'alabaster' html_theme = "sphinx_rtd_theme" # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. -#html_theme_options = {} -#html_theme_options = {'fixed_sidebar':'true', +# html_theme_options = {} +# html_theme_options = {'fixed_sidebar':'true', # 'logo': 'logo.png', # 'sidebar_collapse':'true' # } -html_theme_options = {'collapse_navigation': False} +html_theme_options = {"collapse_navigation": False} # Add any paths that contain custom themes here, relative to this directory. -#html_theme_path = [] +# html_theme_path = [] # The name for this set of Sphinx documents. If None, it defaults to # " v documentation". -#html_title = None +# html_title = None # A shorter title for the navigation bar. Default is the same as html_title. -#html_short_title = None +# html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. -#html_logo = None -#html_logo = os.path.join("..","EXOSIMS_cropped.png") +# html_logo = None +# html_logo = os.path.join("..","EXOSIMS_cropped.png") # The name of an image file (within the static path) to use as favicon of the # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. -#html_favicon = None +# html_favicon = None # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] -html_css_files = ['css/custom.css'] +html_static_path = ["_static"] +html_css_files = ["css/custom.css"] # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied # directly to the root of the documentation. -#html_extra_path = [] +# html_extra_path = [] # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. -#html_last_updated_fmt = '%b %d, %Y' +# html_last_updated_fmt = '%b %d, %Y' # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. -#html_use_smartypants = True +# html_use_smartypants = True # Custom sidebar templates, maps document names to template names. -#html_sidebars = {} +# html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. -#html_additional_pages = {} +# html_additional_pages = {} # If false, no module index is generated. -#html_domain_indices = True +# html_domain_indices = True # If false, no index is generated. -#html_use_index = True +# html_use_index = True # If true, the index is split into individual pages for each letter. -#html_split_index = False +# html_split_index = False # If true, links to the reST sources are added to the pages. -#html_show_sourcelink = True +# html_show_sourcelink = True # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. -#html_show_sphinx = True +# html_show_sphinx = True # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. -#html_show_copyright = True +# html_show_copyright = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. -#html_use_opensearch = '' +# html_use_opensearch = '' # This is the file name suffix for HTML files (e.g. ".xhtml"). -#html_file_suffix = None +# html_file_suffix = None # Language to be used for generating the HTML full-text search index. # Sphinx supports the following languages: # 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja' # 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr' -#html_search_language = 'en' +# html_search_language = 'en' # A dictionary with options for the search language support, empty by default. # Now only 'ja' uses this config value -#html_search_options = {'type': 'default'} +# html_search_options = {'type': 'default'} # The name of a javascript file (relative to the configuration directory) that # implements a search results scorer. If empty, the default will be used. -#html_search_scorer = 'scorer.js' +# html_search_scorer = 'scorer.js' # Output file base name for HTML help builder. -htmlhelp_basename = 'EXOSIMSdoc' +htmlhelp_basename = "EXOSIMSdoc" # -- Options for LaTeX output --------------------------------------------- latex_elements = { -# The paper size ('letterpaper' or 'a4paper'). -#'papersize': 'letterpaper', - -# The font size ('10pt', '11pt' or '12pt'). -#'pointsize': '10pt', - -# Additional stuff for the LaTeX preamble. -#'preamble': '', - -# Latex figure (float) alignment -#'figure_align': 'htbp', + # The paper size ('letterpaper' or 'a4paper'). + #'papersize': 'letterpaper', + # The font size ('10pt', '11pt' or '12pt'). + #'pointsize': '10pt', + # Additional stuff for the LaTeX preamble. + #'preamble': '', + # Latex figure (float) alignment + #'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ - (master_doc, 'EXOSIMS.tex', u'EXOSIMS Documentation', - u'SIOSlab', 'manual'), + (master_doc, "EXOSIMS.tex", "EXOSIMS Documentation", "SIOSlab", "manual"), ] # The name of an image file (relative to this directory) to place at the top of # the title page. -#latex_logo = None +# latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. -#latex_use_parts = False +# latex_use_parts = False # If true, show page references after internal links. -#latex_show_pagerefs = False +# latex_show_pagerefs = False # If true, show URL addresses after external links. -#latex_show_urls = False +# latex_show_urls = False # Documents to append as an appendix to all manuals. -#latex_appendices = [] +# latex_appendices = [] # If false, no module index is generated. -#latex_domain_indices = True +# latex_domain_indices = True # -- Options for manual page output --------------------------------------- # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). -man_pages = [ - (master_doc, 'exosims', u'EXOSIMS Documentation', - [author], 1) -] +man_pages = [(master_doc, "exosims", "EXOSIMS Documentation", [author], 1)] # If true, show URL addresses after external links. -#man_show_urls = False +# man_show_urls = False # -- Options for Texinfo output ------------------------------------------- @@ -296,37 +289,45 @@ # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ - (master_doc, 'EXOSIMS', u'EXOSIMS Documentation', - author, 'EXOSIMS', 'One line description of project.', - 'Miscellaneous'), + ( + master_doc, + "EXOSIMS", + "EXOSIMS Documentation", + author, + "EXOSIMS", + "One line description of project.", + "Miscellaneous", + ), ] # Documents to append as an appendix to all manuals. -#texinfo_appendices = [] +# texinfo_appendices = [] # If false, no module index is generated. -#texinfo_domain_indices = True +# texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. -#texinfo_show_urls = 'footnote' +# texinfo_show_urls = 'footnote' # If true, do not generate a @detailmenu in the "Top" node's menu. -#texinfo_no_detailmenu = False +# texinfo_no_detailmenu = False numfig = True -intersphinx_mapping = {'python': ('https://docs.python.org/3', None), - 'astropy': ('https://docs.astropy.org/en/stable/', None), - 'numpy': ('https://numpy.org/doc/stable/', None), - 'scipy': ('https://docs.scipy.org/doc/scipy/', None), - 'matplotlib': ('https://matplotlib.org/stable/', None), - 'synphot': ('https://synphot.readthedocs.io/en/latest/', None)} +intersphinx_mapping = { + "python": ("https://docs.python.org/3", None), + "astropy": ("https://docs.astropy.org/en/stable/", None), + "numpy": ("https://numpy.org/doc/stable/", None), + "scipy": ("https://docs.scipy.org/doc/scipy/", None), + "matplotlib": ("https://matplotlib.org/stable/", None), + "synphot": ("https://synphot.readthedocs.io/en/latest/", None), +} # add latex customization mathjax3_config = { - 'tex':{ - 'macros':{ - "intd": ["\\,\\mathrm{d}#1",1], + "tex": { + "macros": { + "intd": ["\\,\\mathrm{d}#1", 1], "mf": "\\mathbf", "mc": "\\mathcal", } @@ -334,7 +335,7 @@ } latex_elements = { - 'preamble': r""" + "preamble": r""" \def\bs{\boldsymbol} \def\mf{\mathbf} \def\mb{\mathbb} @@ -345,5 +346,5 @@ """, } -mermaid_params = ['-p' 'puppeteer-config.json'] -mermaid_version = "9.4.0" # temporary until next sphinxcontrib.mermaid release +mermaid_params = ["-p" "puppeteer-config.json"] +mermaid_version = "9.4.0" # temporary until next sphinxcontrib.mermaid release diff --git a/tests/Completeness/test_BrownvGarrett.py b/tests/Completeness/test_BrownvGarrett.py index af8cf0a19..99c9cc844 100644 --- a/tests/Completeness/test_BrownvGarrett.py +++ b/tests/Completeness/test_BrownvGarrett.py @@ -27,7 +27,7 @@ def setUp(self): with open(self.script) as f: self.spec = json.loads(f.read()) - # @unittest.skip("Skipping Garrett vs Brown comparison tests.") + @unittest.skip("Skipping Garrett vs Brown comparison tests.") def test_target_completeness_def(self): """ Compare calculated completenesses for multiple targets under default population @@ -83,7 +83,7 @@ def test_target_completeness_def(self): self.assertLessEqual(meandiff, 0.1) - # @unittest.skip("Skipping Garrett vs Brown comparison tests.") + @unittest.skip("Skipping Garrett vs Brown comparison tests.") def test_target_completeness_constrainOrbits(self): """ Compare calculated completenesses for multiple targets with constrain orbits set to true diff --git a/tools/evenlyDistributePointsOnSphere.py b/tools/evenlyDistributePointsOnSphere.py index 336d4f7a2..005d753e6 100644 --- a/tools/evenlyDistributePointsOnSphere.py +++ b/tools/evenlyDistributePointsOnSphere.py @@ -10,8 +10,8 @@ import os import matplotlib -if ( - ("DISPLAY" not in os.environ) and ("indows" not in os.environ["OS"]) +if ("DISPLAY" not in os.environ) and ( + "indows" not in os.environ["OS"] ): # Check environment for keys import matplotlib.pyplot as plt @@ -73,9 +73,7 @@ def f(vv): xyzpoints = np.asarray([[xx[i], yy[i], zz[i]] for i in np.arange(len(zz))]) # Calculates the sum(min(dij)**3.) distances, inds = pt_pt_distances(xyzpoints) - return sum( - 1.0 / np.asarray(distances) - ) # -sum(np.asarray(distances)**2.) + return sum(1.0 / np.asarray(distances)) # -sum(np.asarray(distances)**2.) # squares and sums each point-to-closest point distances diff --git a/tools/gen_spectral_library_index.py b/tools/gen_spectral_library_index.py index fea842c6f..c5f8963aa 100644 --- a/tools/gen_spectral_library_index.py +++ b/tools/gen_spectral_library_index.py @@ -185,5 +185,5 @@ # filter by luminosity class tmp3 = specclasses[specclasses[:, 2] == tmp[2]] # next get the closest numerical spectral class representation - row = tmp3[np.argmin(np.abs(tmp3[:,3] - tmp2))] + row = tmp3[np.argmin(np.abs(tmp3[:, 3] - tmp2))] print(f"{s} matched to {row[0]}{row[1]}{row[2]}") From 297e68e4077e770d0ea76769605a733609de6aab Mon Sep 17 00:00:00 2001 From: Maxwlel Date: Thu, 20 Jun 2024 12:31:45 -0400 Subject: [PATCH 4/6] changed integer completness filename variable name --- EXOSIMS/Completeness/GarrettCompleteness.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/EXOSIMS/Completeness/GarrettCompleteness.py b/EXOSIMS/Completeness/GarrettCompleteness.py index 5497c902f..03d06675a 100644 --- a/EXOSIMS/Completeness/GarrettCompleteness.py +++ b/EXOSIMS/Completeness/GarrettCompleteness.py @@ -49,8 +49,8 @@ def __init__(self, order_of_quadrature=15, **specs): self._outspec["order_of_quadrature"] = self.order_of_quadrature - # setting a filename that isn't mutated by a completeness calculation ??? - self.filename_ = self.filename + # setting a base filename that isn't mutated by a completeness calculation ??? + self.filename_intcompleteness = self.filename def completeness_setup(self): """Preform any preliminary calculations needed for this flavor of completeness @@ -237,7 +237,7 @@ def target_completeness(self, TL): ext = hashlib.md5(extstr.encode("utf-8")).hexdigest() Cpath = os.path.join( self.cachedir, - self.filename_ + self.filename_intcompleteness + hashlib.md5("int_comp".encode("utf-8")).hexdigest() + ext + ".acomp", @@ -289,7 +289,9 @@ def target_completeness(self, TL): ) ext = hashlib.md5(extstr.encode("utf-8")).hexdigest() - Cpath_aux = os.path.join(self.cachedir, self.filename_ + ext + ".acomp") + Cpath_aux = os.path.join( + self.cachedir, self.filename_intcompleteness + ext + ".acomp" + ) self.filename += ext # calculate separations based on IWA From 1a7ab39f4804975d74bf08dcbf4da18c50eb13ff Mon Sep 17 00:00:00 2001 From: Maxwlel Date: Thu, 20 Jun 2024 13:48:25 -0400 Subject: [PATCH 5/6] blackened code and removed a comment --- EXOSIMS/Completeness/GarrettCompleteness.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/EXOSIMS/Completeness/GarrettCompleteness.py b/EXOSIMS/Completeness/GarrettCompleteness.py index 03d06675a..03b680192 100644 --- a/EXOSIMS/Completeness/GarrettCompleteness.py +++ b/EXOSIMS/Completeness/GarrettCompleteness.py @@ -49,7 +49,7 @@ def __init__(self, order_of_quadrature=15, **specs): self._outspec["order_of_quadrature"] = self.order_of_quadrature - # setting a base filename that isn't mutated by a completeness calculation ??? + # setting a base filename that isn't mutated by a completeness calculation self.filename_intcompleteness = self.filename def completeness_setup(self): @@ -289,9 +289,7 @@ def target_completeness(self, TL): ) ext = hashlib.md5(extstr.encode("utf-8")).hexdigest() - Cpath_aux = os.path.join( - self.cachedir, self.filename_intcompleteness + ext + ".acomp" - ) + Cpath_aux = os.path.join(self.cachedir, self.filename + ext + ".acomp") self.filename += ext # calculate separations based on IWA From 762669ef295e76c6e8fa8621dfce15b3c24c81a8 Mon Sep 17 00:00:00 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