Merge pull request #62 from steven-murray/pypi

Add workflow to publish to pypi

.coverage

@@ -0,0 +1 @@
+!coverage.py: This is a private format, don't read it directly!{"lines":{"/home/steven/Documents/Projects/halos/HMF/hmf/src/hmf/__init__.py":[1,2,3,4,6,7,12,13,14,15,16,17],"/home/steven/Documents/Projects/halos/HMF/hmf/src/hmf/alternatives/__init__.py":[4],"/home/steven/Documents/Projects/halos/HMF/hmf/src/hmf/alternatives/wdm.py":[8,10,11,12,13,14,15,17,23,47,49,63,83,105,107,109,114,129,138,152,162,163,166,184,186,50,51,57,59,61,192,196,212,214,216,220,236,238,240,244,260,262,264,273,284,287,297,313,322,338,349,356,368,370,376,394,401],"/home/steven/Documents/Projects/halos/HMF/hmf/src/hmf/density_field/__init__.py":[4,5,6],"/home/steven/Documents/Projects/halos/HMF/hmf/src/hmf/density_field/transfer.py":[7,8,9,10,11,12,13,15,16,18,23,44,48,49,50,51,52,53,54,55,56,57,58,59,94,110,119,140,149,160,173,182,191,200,209,231,236,243,250,257,270,275,282,287,292,297,305,310,317,326],"/home/steven/Documents/Projects/halos/HMF/hmf/src/hmf/_internals/__init__.py":[3],"/home/steven/Documents/Projects/halos/HMF/hmf/src/hmf/_internals/_cache.py":[8,9,10,13,21,131,138,175,262,176,178,243,245,256,257,260,50,52,112,114,128,180,18,183,187,194,195,196,197,199,201,246,247,250,203,205,206,209,211,213,216,217,218,219,222,132,133,224,229,233,235,188,253,54,57,58,59,60,65,70,74,84,85,87,90,93,251,94,97,98,101,102,103,105,108,110,202,66,67,71,225,236,75,76,79,81],"/home/steven/Documents/Projects/halos/HMF/hmf/src/hmf/density_field/halofit.py":[8,9,10,11,12,13,14,17,106],"/home/steven/Documents/Projects/halos/HMF/hmf/src/hmf/cosmology/__init__.py":[3,4,5],"/home/steven/Documents/Projects/halos/HMF/hmf/src/hmf/cosmology/cosmo.py":[12,14,15,16,17,20,41,43,51,69,90,98,110,45,48,59,60,119,120,49,85,96,62,67,104,105],"/home/steven/Documents/Projects/halos/HMF/hmf/src/hmf/_internals/_framework.py":[3,4,5,11,23,25,27,41,56,74,88,90,93,106,112,113,133,141,152,158,184,185,29,37,38,91,98,99,100,101,103],"/home/steven/Documents/Projects/halos/HMF/hmf/src/hmf/cosmology/growth_factor.py":[8,10,11,12,13,14,15,17,18,20,25,28,30,35,55,56,58,66,106,122,149,165,189,190,205,207,209,216,225,271,298,299,316,318,320,337,354,380,382,383,389,391,430],"/home/steven/Documents/Projects/halos/HMF/hmf/src/hmf/_internals/_utils.py":[1,4,5,13],"/home/steven/Documents/Projects/halos/HMF/hmf/src/hmf/density_field/transfer_models.py":[6,7,8,9,11,12,13,14,16,17,19,23,26,39,41,43,47,64,82,84,86,112,139,141,157,159,161,206,233,320,326,344,346,348,380,393,395,399,478,482,494,541,554,556,564,594,620,621,623,661,684,685,687,712,713,715],"/home/steven/Documents/Projects/halos/HMF/hmf/src/hmf/density_field/filters.py":[4,6,7,8,9,10,11,14,57,59,65,79,95,118,141,159,193,206,220,257,272,273,299,301,305,308,311,314,322,323,349,351,354,357,360,363,367,368,399,400,402,406,409,412,417,422,425,451,452,459,461,463,477,483,489,496,503,512,515,522,528,534],"/home/steven/Documents/Projects/halos/HMF/hmf/src/hmf/mass_function/__init__.py":[3,4],"/home/steven/Documents/Projects/halos/HMF/hmf/src/hmf/mass_function/hmf.py":[6,8,9,10,11,12,13,15,16,17,18,19,20,22,25,66,70,71,72,73,74,75,76,77,78,79,100,109,118,127,141,150,169,185,194,210,219,224,232,246,251,256,261,266,271,284,289,296,328,333,349,356,407,414,421,465,479,493,514],"/home/steven/Documents/Projects/halos/HMF/hmf/src/hmf/mass_function/fitting_functions.py":[6,8,9,10,11,12,13,14,15,18,63,73,74,75,76,77,78,79,80,81,113,137,177,203,204,205,208,210,213,224,305,310,315,320,325,333,339,341,342,344,345,347,122,132,133,349,354,356,357,359,360,361,363,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,85,86,87,88,89,90,91,92,94,95,96,97,98,99,101,104,105,106,107,108,109,110,383,397,405,408,410,413,415,417,418,419,420,422,423,424,425,426,427,428,429,430,431,432,433,434,435,438,439,442,446,454,456,457,459,460,461,463,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,483,484,485,486,488,489,490,491,492,493,494,497,507,512,514,516,517,518,520,522,523,524,525,526,527,528,529,530,531,532,533,534,535,536,537,540,547,552,553,554,556,557,558,560,562,563,565,566,567,568,569,570,571,572,573,574,575,576,577,579,580,581,582,583,585,586,587,588,589,590,591,592,593,594,595,596,597,599,600,601,602,603,604,605,608,629,634,635,636,638,639,640,641,643,644,646,660,665,666,667,668,669,670,672,673,674,675,676,677,678,679,680,681,682,683,684,685,686,687,690,699,704,705,706,709,710,712,713,714,716,717,718,719,720,721,722,723,724,725,726,727,728,729,730,731,734,739,740,741,742,744,745,746,748,749,750,751,754,755,756,757,758,759,760,761,762,763,764,765,766,767,768,769,770,771,772,773,774,775,776,777,780,809,844,849,850,852,853,855,856,857,858,859,860,861,862,863,866,867,868,869,870,871,872,873,874,875,876,877,878,879,880,881,884,892,897,898,899,900,901,903,904,905,906,907,908,909,910,911,912,913,914,915,916,917,918,921,926,927,928,930,931,932,934,935,936,937,938,939,942,943,944,945,946,947,948,949,950,951,952,953,954,955,956,958,959,960,961,965,970,988,993,994,995,997,998,999,1001,1003,1004,1005,1006,1007,1008,1009,1010,1011,1012,1013,1014,1015,1016,1017,1018,1019,1020,1023,1024,102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.flake8

@@ -16,4 +16,21 @@ exclude =
 per-file-ignores =
     scripts/hmf: F821
     scripts/hmf-fit: F821
-select = B,C,E,F,W,T4,B9
+select = B,C,E,F,W,T4,B9,D
+rst-roles =
+    class
+    func
+    mod
+    data
+    const
+    meth
+    attr
+    exc
+    obj
+rst-directives =
+    note
+    warning
+    versionadded
+    versionchanged
+    deprecated
+    seealso

.github/workflows/bump_version.yaml

@@ -1,15 +1,15 @@
-name: Bump version
+name: Bump Version and Deploy
 on:
   push:
     branches:
       - master
 jobs:
-  build:
+  bump-version-and-deploy:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@master
       - name: Bump version and push tag
         uses: mathieudutour/github-tag-action@v4.2
         with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
+          github_token: ${{ secrets.bump_version }}
           default_bump: false

.github/workflows/publish-to-pypi.yaml

@@ -0,0 +1,34 @@
+name: Deploy
+
+on:
+  push:
+    tags:
+      - v*
+
+jobs:
+  build-n-publish:
+    name: To PyPI and TestPyPI
+    runs-on: ubuntu-18.04
+    steps:
+      - uses: actions/checkout@master
+      # https://github.com/ansible/pylibssh/blob/1e7b17f/.github/workflows/build-test-n-publish.yml#L146-L151
+      - name: Get history and tags for SCM versioning to work
+        run: |
+          git fetch --prune --unshallow
+          git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+          git describe --tags
+          git describe --tags $(git rev-list --tags --max-count=1)
+      - name: Set up Python 3.7
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.7
+      - name: Install pep517
+        run: |
+          python -m pip install pep517 --user
+          python setup.py --version
+      - name: Build a binary wheel and a source tarball
+        run: python -m pep517.build --binary --source --out-dir dist .
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          password: ${{ secrets.pypi_password }}

.github/workflows/publish-to-test-pypi.yaml

@@ -0,0 +1,32 @@
+name: Deploy to Test PyPI
+
+on: push
+
+jobs:
+  build-n-publish:
+    name: Deploy
+    runs-on: ubuntu-18.04
+    steps:
+      - uses: actions/checkout@master
+      # https://github.com/ansible/pylibssh/blob/1e7b17f/.github/workflows/build-test-n-publish.yml#L146-L151
+      - name: Get history and tags for SCM versioning to work
+        run: |
+          git fetch --prune --unshallow
+          git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+          git describe --tags
+          git describe --tags $(git rev-list --tags --max-count=1)
+      - name: Set up Python 3.7
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.7
+      - name: Install pep517
+        run: |
+          python -m pip install pep517 --user
+          python setup.py --version
+      - name: Build a binary wheel and a source tarball
+        run: python -m pep517.build --binary --source --out-dir dist .
+      - name: Publish distribution 📦 to Test PyPI
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          password: ${{ secrets.test_pypi_password }}
+          repository_url: https://test.pypi.org/legacy/

.pre-commit-config.yaml

@@ -21,7 +21,13 @@ repos:
     rev: '3.8.1'  # pick a git hash / tag to point to
     hooks:
     -   id: flake8
+        additional_dependencies:
+          - flake8-rst-docstrings
 -   repo: https://github.com/psf/black
     rev: 19.10b0
     hooks:
     - id: black
+-   repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.5.1
+    hooks:
+      - id: rst-backticks

CHANGELOG.rst

@@ -21,7 +21,7 @@ of this.
 
 - When using camb for the transfer function, some cosmologies would lead to a segfault (i.e. when Ob0 or Tcmb0 are not
   set explicitly). This now raises a helpful error.
-- Fixed bug in ordering of iterator in `get_hmf`.
+- Fixed bug in ordering of iterator in ``get_hmf``.
 
 **Internals**
 
@@ -40,7 +40,8 @@ v3.0.8 [26th March 2020]
 
 **Enhancement**
 
-- Added `get_dependencies` method to _Framework, to enable finding all parameters that a quantity depends on.
+- Added ``get_dependencies`` method to _Framework, to enable finding all parameters that
+  a quantity depends on.
 - Growth factor speed-up (thanks to @jlashner)
 - Added use_splined_growth argument (thanks to @jlashner)
 
@@ -56,10 +57,10 @@ v3.0.5 [23rd April 2019]
 ------------------------
 **Bugfixes**
 
-- Fixed naming of WDM `alter_dndm` to `alter_model` to be consistent.
+- Fixed naming of WDM ``alter_dndm`` to ``alter_model`` to be consistent.
 - Fixed bug which made CAMB transfer function not pickleable or copyable.
   NOTE: the fix is not perfect -- if you provide a custom CAMBparams class
-        to `transfer_params`, it is not certain that results will be consistent,
+        to ``transfer_params``, it is not certain that results will be consistent,
         as a few of the attributes of this object are not pickleable, and thus
         are ignored.
 
@@ -200,15 +201,15 @@ are buggy and untested. Don't use these until the next version unless you're cra
 **Enhancments**
 
 - Removed nz and z2 from MassFunction. They will return in a later version but better.
-- Improved structure for FittingFunction Component, with `cutmask` property defining valid mass range. NOTE: the default
+- Improved structure for FittingFunction Component, with ``cutmask`` property defining valid mass range. NOTE: the default
   MassFunction is no longer to mask values outside the valid range. In fact, the parameter ``cut_fit`` no longer exists.
   One can achieve the effect by accessing a relevant array as dndm[MassFunction.hmf.cutmask]
 - Renamed some parameters/quantities for more consistency (esp. M --> m)
 - No longer dependent on cosmolopy, but rather uses Astropy (v1.0+)
-- `mean_dens` now `mean_density0`, as per Astropy
+- ``mean_dens`` now ``mean_density0``, as per Astropy
 - Added exception to catch when dndm has many NaN values in it.
 - Many more tests
-- Made the `cosmo` class pickleable by cutting out a method and using it as a function instead.
+- Made the ``cosmo`` class pickleable by cutting out a method and using it as a function instead.
 - Added normalise() to Transfer class.
 - Updated fit.py extensively, and provided new example config files
 - Send arbitrary kwargs to downhill solver
@@ -444,7 +445,7 @@ v1.8.0 [February 2, 2015]
 
 - A few more documentation updates (especially tools.py)
 - Removed new_k_bounds function from tools.py
-- Added `w` parameter to cosmolopy dictionary in `cosmo.py`
+- Added ``w`` parameter to cosmolopy dictionary in ``cosmo.py``
 - Changed cosmography significantly to use cosmolopy in general
 - Generally tidied up some of the update mechanisms.
 - **API CHANGE**: cosmography.py no longer exists -- I've chosen to utilise

CONTRIBUTING.rst

@@ -57,7 +57,7 @@ advice to help make your work on hmf more useful and rewarding.
 
 * Use issue labels to guide you
   - Unsure where to begin contributing to hmf? You can start by looking through issues
-    labeled `good first issue` and `help wanted` issues.
+    labeled ``good first issue`` and ``help wanted`` issues.
 * Pick a subject area that you care about, that you are familiar with, or that you want
   to learn about
   - There are many aspects to hmf, from cosmography, through cosmological initial
@@ -95,9 +95,9 @@ Getting started
 5. If you like the change and think the project could use it:
   - If you're fixing a bug, include a new test that breaks as a result of the bug (if possible).
   - Ensure that all your new code is covered by tests and that the existing tests pass.
-    Tests can be run by running `pytest` in the top level ``hmf`` directory.
+    Tests can be run by running ``pytest`` in the top level ``hmf`` directory.
   - Ensure that you fully document any new features via docstrings, and potentially
-    as a new tutorial in the `docs/` directory.
+    as a new tutorial in the ``docs/`` directory.
 6. Make a Pull Request from your fork/branch.
 
 Code review process

README.rst

@@ -15,7 +15,7 @@ hmf
 .. image:: https://img.shields.io/badge/code%20style-black-000000.svg
     :target: https://github.com/psf/black
 
-`hmf` is a python application that provides a flexible and simple way to calculate the
+``hmf`` is a python application that provides a flexible and simple way to calculate the
 Halo Mass Function for a range of varying parameters. It is also the backend to
 `HMFcalc <http://hmf.icrar.org>`_, the online HMF calculator.
 
@@ -55,7 +55,7 @@ From v3.1, ``hmf`` supports Python 3.6+, and has dropped support for Python 2.
 
 Quickstart
 ----------
-Once you have `hmf` installed, you can quickly generate a mass function
+Once you have ``hmf`` installed, you can quickly generate a mass function
 by opening an interpreter (e.g. IPython/Jupyter) and doing::
 
     >>> from hmf import MassFunction
@@ -64,7 +64,7 @@ by opening an interpreter (e.g. IPython/Jupyter) and doing::
 
 Note that all parameters have (what I consider reasonable) defaults. In particular,
 this will return a Tinker (2008) mass function between
-:math:`10^{10}-10^{15} M_\odot`, at :math:`z=0` for the default PLANCK15 cosmology.
+10^10 and 10^15 solar masses, at z=0 for the default PLANCK15 cosmology.
 Nevertheless, there are several parameters which can be input, either cosmological
 or otherwise. The best way to see these is to do::
 
@@ -75,13 +75,13 @@ We can also check which parameters have been set in our "default" instance::
     >>> hmf.parameter_values
 
 To change the parameters (cosmological or otherwise), one should use the
-`update()` method, if a MassFunction() object already exists. For example::
+``update()`` method, if a MassFunction() object already exists. For example::
 
     >>> hmf = MassFunction()
     >>> hmf.update(cosmo_params={"Ob0": 0.05}, z=10) #update baryon density and redshift
     >>> cumulative_mass_func = hmf.ngtm
 
-For a more involved introduction to `hmf`, check out the `tutorials <tutorials.html>`_,
+For a more involved introduction to ``hmf``, check out the `tutorials <tutorials.html>`_,
 which are currently under construction, or the `API docs <api.html>`_.
 
 Versioning

docs/index.rst

@@ -1,7 +1,7 @@
 .. hmf documentation master file, created by
    sphinx-quickstart on Mon Dec  2 10:40:08 2013.
    You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
+   contain the root "toctree" directive.
 
 .. include:: ../README.rst
 

pyproject.toml

@@ -1,4 +1,6 @@
 [build-system]
 requires = ["setuptools>=42", "wheel", "setuptools_scm[toml]>=3.4"]
+build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
+local_scheme = "no-local-version"

scripts/hmf

@@ -15,7 +15,7 @@ import sys
 import os
 import traceback
 
-import hmf
+from src import hmf
 import numpy as np
 from argparse import ArgumentParser
 from argparse import RawDescriptionHelpFormatter
@@ -101,7 +101,7 @@ USAGE
                             help="the mass range and intervals, min max step [default: %s %s %s]" %
                             (np.log10(h.M[0]), np.log10(h.M[-1]), np.log10(h.M[1]) - np.log10(h.M[0])))
         hmfargs.add_argument("--mf-fit", nargs="*", choices=hmf.Fits.mf_fits + ["all"],
-                            help="fitting function(s) to use. 'all' uses all of them [default: %s]" % h.mf_fit)
+                             help="fitting function(s) to use. 'all' uses all of them [default: %s]" % h.mf_fit)
         hmfargs.add_argument("--delta-h", nargs="*", type=float,
                             help="overdensity of halo w.r.t delta_wrt [default %s]" % h.delta_wrt)
         hmfargs.add_argument("--delta-wrt", choices=["mean", "crit"],

scripts/hmf-fit

@@ -17,14 +17,7 @@ from argparse import ArgumentParser
 from argparse import RawDescriptionHelpFormatter
 from ConfigParser import SafeConfigParser as cfg
 cfg.optionxform = str
-import time
-import errno
-from os.path import join
-from numbers import Number
-import pickle
-from emcee import autocorr
-from importlib import import_module
-from hmf.fitting import cli_tools as cli
+from fitting import cli_tools as cli
 
 __all__ = []
 __version__ = 0.5