Docs commit?

Jenkinsfile

@@ -15,7 +15,7 @@ pipeline {
 	environment {
 		POETRY_HOME="/opt/poetry"
 		POETRY_VERSION="1.1.4"
-		//PYPI=credentials("DOES_NOT_EXIST")
+		PYPI=credentials("pypi-pysuperconductor")
 	}
 
 	stages {
@@ -53,7 +53,7 @@ pipeline {
 			}
 			steps {
 				echo 'Deploying...'
-				// sh '${POETRY_HOME}/bin/poetry publish -u ${PYPI_USR} -p ${PYPI_PSW} --build'
+				sh '${POETRY_HOME}/bin/poetry publish -u ${PYPI_USR} -p ${PYPI_PSW} --build'
 			}
 		}
 	}
@@ -63,7 +63,7 @@ pipeline {
 			junit 'pytest.xml'
 			cobertura coberturaReportFile: 'coverage.xml'
 			mail (bcc: '',
-				body: "Project: ${env.JOB_NAME} <br>Build Number: ${env.BUILD_NUMBER} <br> Build URL: ${env.BUILD_URL}", cc: '', charset: 'UTF-8', from: 'jenkins@jenkins.deepak.science', mimeType: 'text/html', replyTo: 'dmallubhotla+jenkins@gmail.com', subject: "CI ${currentBuild.currentResult}: Project name -> ${env.JOB_NAME}", to: "dmallubhotla+ci@gmail.com")
+				body: "Project: ${env.JOB_NAME} <br>Build Number: ${env.BUILD_NUMBER} <br> Build URL: ${env.BUILD_URL}", cc: '', charset: 'UTF-8', from: 'jenkins@jenkins.deepak.science', mimeType: 'text/html', replyTo: 'dmallubhotla+jenkins@gmail.com', subject: "${env.JOB_NAME} #${env.BUILD_NUMBER}: Build ${currentBuild.currentResult}", to: "dmallubhotla+ci@gmail.com")
 		}
 		success {
 			echo 'This will run only if successful'

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -0,0 +1,52 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# 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.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'pysuperconductor'
+copyright = '2021, Deepak Mallubhotla'
+author = 'Deepak Mallubhotla'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# 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']

docs/index.rst

@@ -0,0 +1,20 @@
+.. pysuperconductor documentation master file, created by
+   sphinx-quickstart on Mon Jan  4 16:01:14 2021.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to pysuperconductor's documentation!
+============================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pysuperconductor"
-version = "0.1.0"
+version = "0.1.1"
 description = ""
 authors = ["Deepak <dmallubhotla+github@gmail.com>"]
 

pysuperconductor/__init__.py

@@ -1,3 +1,8 @@
+"""pysuperconductor
+
+This package implements some superconductor calculations, to facilitate noise
+calculations in proximity to superconductors.
+"""
 import logging
 from pysuperconductor.meta import __version__
 

pysuperconductor/os_gap_calc.py

@@ -1,9 +1,16 @@
 import numpy  # type: ignore
 import scipy.integrate as integrate  # type: ignore
 import scipy.optimize  # type: ignore
+import scipy.special  # type: ignore
+import logging
+import warnings
+
+from typing import Tuple
 
 
 def energy(freq: float, delta: float) -> float:
+	"""Takes in a "raw" quasiparticle energy and a gap, and returns the
+	quasiparticle's energy in the SC state."""
 	return numpy.sqrt(freq ** 2 + delta ** 2)
 
 
@@ -32,11 +39,16 @@ def gap_integral(
 	return integrate.quad(integrand, 0, debye_frequency)[0]
 
 
-def equilibrium_gap(temp, debye_frequency, nv):
+def equilibrium_gap(temp: float, debye_frequency: float, nv: float) -> float:
 	return find_gap(temp, 0, debye_frequency, nv)
 
 
-def find_gap(temp, mu_star, debye_frequency, nv):
+def find_gap(
+	temp: float,
+	mu_star: float,
+	debye_frequency: float,
+	nv: float
+) -> float:
 	nv_inv = 1 / nv
 	sol = scipy.optimize.root(
 		lambda d: gap_integral(temp, d, mu_star, debye_frequency) - nv_inv,
@@ -46,18 +58,44 @@ def find_gap(temp, mu_star, debye_frequency, nv):
 
 
 # this is n * Delta_0, calling it n in this file for brevity
-def n_integrand_function(xi, temp, delta, mu_star):
+def n_integrand_function(
+	xi: float, temp: float, delta: float, mu_star: float
+) -> float:
 	big_e = energy(xi, delta)
-	left = 1 / (1 + numpy.exp((big_e - mu_star) / temp))
-	right = 1 / (1 + numpy.exp(big_e / temp))
+	left = scipy.special.expit((mu_star - big_e) / temp)
+	right = scipy.special.expit(- big_e / temp)
 	return left - right
 
 
 # as above, this is brevity n * Delta_0
-def n_integral(temp, delta, mu_star):
-	def integrand(xi):
+def n_integral(temp: float, delta: float, mu_star: float) -> float:
+	def integrand(xi: float) -> float:
 		return n_integrand_function(xi, temp, delta, mu_star)
 	intermediate = 20 * numpy.sqrt(delta ** 2 + mu_star ** 2)
 	lower = integrate.quad(integrand, 0, intermediate)[0]
 	upper = integrate.quad(integrand, intermediate, numpy.inf)[0]
 	return lower + upper
+
+
+def find_gap_for_n(
+	temp: float,
+	n_bare: float,
+	debye_frequency: float,
+	nv: float
+) -> Tuple[float, float]:
+	n = n_bare * find_gap(0, 0, debye_frequency, nv)
+	nv_inv = 1 / nv
+	with warnings.catch_warnings():
+		warnings.filterwarnings(
+			"ignore",
+			message="Creating an ndarray from ragged nested"
+		)
+		sol = scipy.optimize.root(
+			lambda x: [
+				gap_integral(temp, x[0], x[1], debye_frequency) - nv_inv,
+				n_integral(temp, x[0], x[1]) - n
+			],
+			x0=[debye_frequency / (numpy.sinh(nv_inv)), 0]
+		)
+		logging.debug(sol)
+		return sol.x

pysuperconductor/sc_free_energy.py

@@ -0,0 +1,9 @@
+def sc_free_energy(
+	delta: float,
+	temp: float,
+	mustar: float,
+	debye_freq: float,
+	n_0: float,
+	v_interaction_0: float
+) -> float:
+	return 9999.35

tests/test_os_gap_calc.py

@@ -67,3 +67,15 @@ def test_n_integral():
 		verbose=True
 	)
 	assert not record
+
+
+def test_find_n_gap():
+	actual = None
+	with pytest.warns(None) as record:
+		actual = pysuperconductor.os_gap_calc.find_gap_for_n(.3, .1, 100, .2)
+	numpy.testing.assert_almost_equal(
+		actual[0], 1.0296692197710933,
+		decimal=7, err_msg="did not find correct delta",
+		verbose=True
+	)
+	assert not record

tests/test_sc_free_energy.py

@@ -0,0 +1,22 @@
+import pysuperconductor.sc_free_energy
+import numpy
+import pytest
+
+
+def test_sc_free_energy():
+	with pytest.warns(None) as record:
+		actual = pysuperconductor.sc_free_energy.sc_free_energy(
+			0.907816, .5, .247777, 100, 1, .2)
+	assert not record
+	numpy.testing.assert_almost_equal(
+		actual, 9999.35,
+		decimal=7, err_msg='superconducting free energy was off', verbose=True
+	)
+	with pytest.warns(None) as record:
+		actual = pysuperconductor.sc_free_energy.sc_free_energy(
+			0.907816, .5, .247777, 50, 1, .2)
+	assert not record
+	# numpy.testing.assert_almost_equal(
+	# 	actual, 2498.910078644398,
+	# 	decimal=7, err_msg='superconducting free energy was off', verbose=True
+	# )