Adds docs

.gitignore

@@ -139,4 +139,7 @@ dmypy.json
 # Cython debug symbols
 cython_debug/
 
-token.txt
+token.txt
+
+#don't care about intellij
+.idea/

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 {
@@ -40,6 +40,11 @@ pipeline {
 						sh '${POETRY_HOME}/bin/poetry run flake8'
 					}
 				}
+				stage('mypy') {
+					steps {
+						sh '${POETRY_HOME}/bin/poetry run mypy pysuperconductor'
+					}
+				}
 			}
 		}
 		stage('Deploy') {
@@ -48,7 +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'
 			}
 		}
 	}
@@ -58,7 +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'

do.sh

@@ -12,6 +12,7 @@ build() {
 test() {
    echo "I am ${FUNCNAME[0]}ing"
    poetry run flake8
+   poetry run mypy pysuperconductor
    poetry run pytest
 }
 

poetry.lock

@@ -1,53 +1,51 @@
 [[package]]
-category = "dev"
-description = "Atomic file writes."
-marker = "sys_platform == \"win32\""
 name = "atomicwrites"
+version = "1.4.0"
+description = "Atomic file writes."
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "1.4.0"
 
 [[package]]
-category = "dev"
-description = "Classes Without Boilerplate"
 name = "attrs"
+version = "20.3.0"
+description = "Classes Without Boilerplate"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "20.3.0"
 
 [package.extras]
-dev = ["coverage (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "furo", "sphinx", "pre-commit"]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "furo", "sphinx", "pre-commit"]
 docs = ["furo", "sphinx", "zope.interface"]
-tests = ["coverage (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"]
-tests_no_zope = ["coverage (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"]
+tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six"]
 
 [[package]]
-category = "dev"
-description = "Cross-platform colored terminal text."
-marker = "sys_platform == \"win32\""
 name = "colorama"
+version = "0.4.4"
+description = "Cross-platform colored terminal text."
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-version = "0.4.4"
 
 [[package]]
-category = "dev"
-description = "Code coverage measurement for Python"
 name = "coverage"
+version = "5.3"
+description = "Code coverage measurement for Python"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4"
-version = "5.3"
 
 [package.extras]
 toml = ["toml"]
 
 [[package]]
-category = "dev"
-description = "the modular source code checker: pep8 pyflakes and co"
 name = "flake8"
+version = "3.8.4"
+description = "the modular source code checker: pep8 pyflakes and co"
+category = "dev"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
-version = "3.8.4"
 
 [package.dependencies]
 mccabe = ">=0.6.0,<0.7.0"
@@ -55,96 +53,120 @@ pycodestyle = ">=2.6.0a1,<2.7.0"
 pyflakes = ">=2.2.0,<2.3.0"
 
 [[package]]
-category = "dev"
-description = "iniconfig: brain-dead simple config-ini parsing"
 name = "iniconfig"
-optional = false
-python-versions = "*"
 version = "1.1.1"
-
-[[package]]
+description = "iniconfig: brain-dead simple config-ini parsing"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "mccabe"
+version = "0.6.1"
+description = "McCabe checker, plugin for flake8"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "mypy"
+version = "0.790"
+description = "Optional static typing for Python"
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
+[package.dependencies]
+mypy-extensions = ">=0.4.3,<0.5.0"
+typed-ast = ">=1.4.0,<1.5.0"
+typing-extensions = ">=3.7.4"
+
+[package.extras]
+dmypy = ["psutil (>=4.0)"]
+
+[[package]]
+name = "mypy-extensions"
+version = "0.4.3"
+description = "Experimental type system extensions for programs checked with the mypy typechecker."
 category = "dev"
-description = "McCabe checker, plugin for flake8"
-name = "mccabe"
 optional = false
 python-versions = "*"
-version = "0.6.1"
 
 [[package]]
-category = "main"
-description = "NumPy is the fundamental package for array computing with Python."
 name = "numpy"
+version = "1.19.3"
+description = "NumPy is the fundamental package for array computing with Python."
+category = "main"
 optional = false
 python-versions = ">=3.6"
-version = "1.19.4"
 
 [[package]]
-category = "dev"
-description = "Core utilities for Python packages"
 name = "packaging"
+version = "20.4"
+description = "Core utilities for Python packages"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "20.4"
 
 [package.dependencies]
 pyparsing = ">=2.0.2"
 six = "*"
 
 [[package]]
-category = "dev"
-description = "plugin and hook calling mechanisms for python"
 name = "pluggy"
+version = "0.13.1"
+description = "plugin and hook calling mechanisms for python"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "0.13.1"
 
 [package.extras]
 dev = ["pre-commit", "tox"]
 
 [[package]]
-category = "dev"
-description = "library with cross-python path, ini-parsing, io, code, log facilities"
 name = "py"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 version = "1.9.0"
+description = "library with cross-python path, ini-parsing, io, code, log facilities"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
-category = "dev"
-description = "Python style guide checker"
 name = "pycodestyle"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 version = "2.6.0"
-
-[[package]]
+description = "Python style guide checker"
 category = "dev"
-description = "passive checker of Python programs"
-name = "pyflakes"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "2.2.0"
 
 [[package]]
+name = "pyflakes"
+version = "2.2.0"
+description = "passive checker of Python programs"
 category = "dev"
-description = "Python parsing module"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+
+[[package]]
 name = "pyparsing"
+version = "2.4.7"
+description = "Python parsing module"
+category = "dev"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
-version = "2.4.7"
 
 [[package]]
-category = "dev"
-description = "pytest: simple powerful testing with Python"
 name = "pytest"
+version = "6.1.2"
+description = "pytest: simple powerful testing with Python"
+category = "dev"
 optional = false
 python-versions = ">=3.5"
-version = "6.1.2"
 
 [package.dependencies]
-atomicwrites = ">=1.0"
+atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
 attrs = ">=17.4.0"
-colorama = "*"
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
 iniconfig = "*"
 packaging = "*"
 pluggy = ">=0.12,<1.0"
@@ -152,55 +174,71 @@ py = ">=1.8.2"
 toml = "*"
 
 [package.extras]
-checkqa_mypy = ["mypy (0.780)"]
+checkqa_mypy = ["mypy (==0.780)"]
 testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]
 
 [[package]]
-category = "dev"
-description = "Pytest plugin for measuring coverage."
 name = "pytest-cov"
+version = "2.10.1"
+description = "Pytest plugin for measuring coverage."
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-version = "2.10.1"
 
 [package.dependencies]
 coverage = ">=4.4"
 pytest = ">=4.6"
 
 [package.extras]
-testing = ["fields", "hunter", "process-tests (2.0.2)", "six", "pytest-xdist", "virtualenv"]
+testing = ["fields", "hunter", "process-tests (==2.0.2)", "six", "pytest-xdist", "virtualenv"]
 
 [[package]]
-category = "main"
-description = "SciPy: Scientific Library for Python"
 name = "scipy"
+version = "1.5.4"
+description = "SciPy: Scientific Library for Python"
+category = "main"
 optional = false
 python-versions = ">=3.6"
-version = "1.5.4"
 
 [package.dependencies]
 numpy = ">=1.14.5"
 
 [[package]]
-category = "dev"
-description = "Python 2 and 3 compatibility utilities"
 name = "six"
+version = "1.15.0"
+description = "Python 2 and 3 compatibility utilities"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
-version = "1.15.0"
 
 [[package]]
-category = "dev"
-description = "Python Library for Tom's Obvious, Minimal Language"
 name = "toml"
+version = "0.10.2"
+description = "Python Library for Tom's Obvious, Minimal Language"
+category = "dev"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
-version = "0.10.2"
+
+[[package]]
+name = "typed-ast"
+version = "1.4.1"
+description = "a fork of Python 2 and 3 ast modules with type comment support"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "typing-extensions"
+version = "3.7.4.3"
+description = "Backported and Experimental Type Hints for Python 3.5+"
+category = "dev"
+optional = false
+python-versions = "*"
 
 [metadata]
-content-hash = "f85e1e6bd82f5fe32bdf92c718d92c82203556d707dd1068d93877e311096773"
-lock-version = "1.0"
+lock-version = "1.1"
 python-versions = "^3.8"
+content-hash = "0a44a1d796f0619dcc526b6bd681fd179a6c888e4d75826de435fee2e7332a25"
 
 [metadata.files]
 atomicwrites = [
@@ -263,41 +301,61 @@ mccabe = [
     {file = "mccabe-0.6.1-py2.py3-none-any.whl", hash = "sha256:ab8a6258860da4b6677da4bd2fe5dc2c659cff31b3ee4f7f5d64e79735b80d42"},
     {file = "mccabe-0.6.1.tar.gz", hash = "sha256:dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f"},
 ]
+mypy = [
+    {file = "mypy-0.790-cp35-cp35m-macosx_10_6_x86_64.whl", hash = "sha256:bd03b3cf666bff8d710d633d1c56ab7facbdc204d567715cb3b9f85c6e94f669"},
+    {file = "mypy-0.790-cp35-cp35m-manylinux1_x86_64.whl", hash = "sha256:2170492030f6faa537647d29945786d297e4862765f0b4ac5930ff62e300d802"},
+    {file = "mypy-0.790-cp35-cp35m-win_amd64.whl", hash = "sha256:e86bdace26c5fe9cf8cb735e7cedfe7850ad92b327ac5d797c656717d2ca66de"},
+    {file = "mypy-0.790-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:e97e9c13d67fbe524be17e4d8025d51a7dca38f90de2e462243ab8ed8a9178d1"},
+    {file = "mypy-0.790-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:0d34d6b122597d48a36d6c59e35341f410d4abfa771d96d04ae2c468dd201abc"},
+    {file = "mypy-0.790-cp36-cp36m-win_amd64.whl", hash = "sha256:72060bf64f290fb629bd4a67c707a66fd88ca26e413a91384b18db3876e57ed7"},
+    {file = "mypy-0.790-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:eea260feb1830a627fb526d22fbb426b750d9f5a47b624e8d5e7e004359b219c"},
+    {file = "mypy-0.790-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:c614194e01c85bb2e551c421397e49afb2872c88b5830e3554f0519f9fb1c178"},
+    {file = "mypy-0.790-cp37-cp37m-win_amd64.whl", hash = "sha256:0a0d102247c16ce93c97066443d11e2d36e6cc2a32d8ccc1f705268970479324"},
+    {file = "mypy-0.790-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:cf4e7bf7f1214826cf7333627cb2547c0db7e3078723227820d0a2490f117a01"},
+    {file = "mypy-0.790-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:af4e9ff1834e565f1baa74ccf7ae2564ae38c8df2a85b057af1dbbc958eb6666"},
+    {file = "mypy-0.790-cp38-cp38-win_amd64.whl", hash = "sha256:da56dedcd7cd502ccd3c5dddc656cb36113dd793ad466e894574125945653cea"},
+    {file = "mypy-0.790-py3-none-any.whl", hash = "sha256:2842d4fbd1b12ab422346376aad03ff5d0805b706102e475e962370f874a5122"},
+    {file = "mypy-0.790.tar.gz", hash = "sha256:2b21ba45ad9ef2e2eb88ce4aeadd0112d0f5026418324176fd494a6824b74975"},
+]
+mypy-extensions = [
+    {file = "mypy_extensions-0.4.3-py2.py3-none-any.whl", hash = "sha256:090fedd75945a69ae91ce1303b5824f428daf5a028d2f6ab8a299250a846f15d"},
+    {file = "mypy_extensions-0.4.3.tar.gz", hash = "sha256:2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8"},
+]
 numpy = [
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@@ -366,3 +424,40 @@ toml = [
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 ]
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pyproject.toml

@@ -1,18 +1,19 @@
 [tool.poetry]
 name = "pysuperconductor"
-version = "0.1.0"
+version = "0.1.1"
 description = ""
 authors = ["Deepak <dmallubhotla+github@gmail.com>"]
 
 [tool.poetry.dependencies]
 python = "^3.8"
 scipy = "^1.5.4"
-numpy = "^1.19.4"
+numpy = "1.19.3"
 
 [tool.poetry.dev-dependencies]
 pytest = ">=6"
 flake8 = "^3.8.4"
 pytest-cov = "^2.10.1"
+mypy = "^0.790"
 
 [tool.pytest.ini_options]
 junit_family = "xunit1"

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

@@ -1,32 +1,54 @@
-import numpy
-import scipy.integrate as integrate
-import scipy.optimize
+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, delta):
+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)
 
 
-def gap_integrand_function(xi, temp, delta, mu_star):
+def gap_integrand_function(
+	xi: float,
+	temp: float,
+	delta: float,
+	mu_star: float
+) -> float:
 	big_e = energy(xi, delta)
 	if temp == 0:
 		return (1 / (2 * big_e)) * (2 * numpy.heaviside(big_e - mu_star, .5) - 1)
 	return numpy.tanh((big_e - mu_star) / (2 * temp)) / (2 * big_e)
 
 
-def gap_integral(temp, delta, mu_star, debye_frequency):
-	def integrand(xi):
+def gap_integral(
+	temp: float,
+	delta: float,
+	mu_star: float,
+	debye_frequency: float
+) -> float:
+	def integrand(xi: float) -> float:
 		# the 2 here is to account for the symmetry in the integration range
 		# to cut the integral to zero to omega_debyeh
 		return 2 * gap_integrand_function(xi, temp, delta, mu_star)
 	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,
@@ -36,18 +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
+	# )