fix: some fixes to errors raised (#94)

* fix: some fixes to errors raised

Emits nicer ValueErrors in a couple of instances, instead of mere assertions.
Also adds some .github YAML configurations for upcoming changes to CD.

* fix: tests that raise a different error now

* docs: update readme badges

* test: add tests of error corner cases

* docs: better python badge

.github/dependabot.yml

@@ -0,0 +1,21 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: "/"
+    schedule:
+      interval: monthly
+  - package-ecosystem: pip
+    directory: "/.github/workflows"
+    schedule:
+      interval: monthly
+  - package-ecosystem: pip
+    directory: "/docs"
+    schedule:
+      interval: monthly
+  - package-ecosystem: pip
+    directory: "/"
+    schedule:
+      interval: monthly
+    versioning-strategy: lockfile-only
+    allow:
+      - dependency-type: "all"

.github/labels.yml

@@ -0,0 +1,85 @@
+---
+# Labels names are important as they are used by Release Drafter to decide
+# regarding where to record them in changelog or if to skip them.
+#
+# The repository labels will be automatically configured using this file and
+# the GitHub Action https://github.com/marketplace/actions/github-labeler.
+- name: "API breaking"
+  description: Breaking Changes
+  color: e305fc
+- name: "good first issue"
+  description: Good for newcomers
+  color: 7057ff
+
+- name: "status: duplicate"
+  description: This issue or pull request already exists
+  color: d93f0b
+- name: "status: invalid"
+  description: Invalid issue or pull request
+  color: d93f0b
+- name: "status: requires discussion"
+  description: Issue requires further discussion before implementation
+  color: f71bd2
+- name: "status: requires research"
+  description: Issue requires further research before implementation
+  color: "d93f0b"
+- name: "status: wontfix"
+  description: Valid issue, but out of scope for future fixes
+  color: "d93f0b"
+
+- name: "type: maint: dependencies"
+  description: Pull requests that update a dependency file
+  color: "0366d6"
+- name: "type: maint: documentation"
+  description: Improvements or additions to documentation
+  color: "0075ca"
+- name: "type: maint: refactoring"
+  description: Refactoring
+  color: ef67c4
+- name: "type: maint: removal"
+  description: Removals and Deprecations
+  color: 9ae7ea
+- name: "type: maint: style"
+  description: Style
+  color: c120e5
+- name: "type: maint: build"
+  description: Build System and Dependencies
+  color: bfdadc
+
+- name: "type: accuracy"
+  description: "Enhancement that improves accuracy"
+  color: "bfd4f2"
+- name: "type: bug"
+  description: Something isn't working
+  color: d73a4a
+- name: "type: feature: ui"
+  description: New feature that adds functionality for the user
+  color: "0e8a16"
+- name: "type: feature: physical"
+  description: New feature that adds new analysis/physical model
+  color: "0e8a16"
+- name: "type: testing"
+  description: Testing improvements
+  color: b1fc6f
+- name: "type: performance: memory"
+  description: Performance improvements that reduce memory usage
+  color: "016175"
+- name: "type: performance: cpu"
+  description: Performance improvements that reduce walltime
+  color: "016175"
+- name: "type: ci"
+  description: Updates to CI (GH actions, RTD, etc.)
+  color: "000000"
+- name: "type: question"
+  description: A question about the code or documentation
+  color: d876e3
+
+- name: "priority: low"
+  description: Low priority
+  color: "BFD4F2"
+- name: "priority: medium"
+  description: Medium priority
+  color: "E99695"
+- name: "priority: high"
+  description: High priority
+  color: "B60205"

.github/release-drafter.yml

@@ -0,0 +1,66 @@
+# See https://github.com/marketplace/actions/release-drafter for configuration
+categories:
+  - title: ":boom: Breaking Changes"
+    label: "breaking"
+  - title: ":rocket: Features"
+    label: "enhancement"
+  - title: ":fire: Removals and Deprecations"
+    label: "removal"
+  - title: ":beetle: Fixes"
+    label: "bug"
+  - title: ":racehorse: Performance"
+    label: "performance"
+  - title: ":rotating_light: Testing"
+    label: "testing"
+  - title: ":construction_worker: Continuous Integration"
+    label: "ci"
+  - title: ":books: Documentation"
+    label: "documentation"
+  - title: ":hammer: Refactoring"
+    label: "refactoring"
+  - title: ":lipstick: Style"
+    label: "style"
+  - title: ":package: Dependencies"
+    labels:
+      - "dependencies"
+      - "build"
+name-template: 'v$RESOLVED_VERSION'
+tag-template: 'v$RESOLVED_VERSION'
+autolabeler:
+  - label: 'documentation'
+    files:
+      - '*.md'
+    branch:
+      - '/.*docs{0,1}.*/'
+  - label: 'bug'
+    branch:
+      - '/fix.*/'
+    title:
+      - '/fix/i'
+  - label: 'enhancement'
+    branch:
+      - '/feature.*|add-.+/'
+    title:
+      - '/feat:.+|feature:.+/i'
+  - label: "removal"
+    title:
+      - "/remove .*/i"
+  - label: "performance"
+    title:
+      - "/.* performance .*/i"
+  - label: "ci"
+    files:
+      - '.github/*'
+      - '.pre-commit-config.yaml'
+      - '.coveragrc'
+  - label: "style"
+    files:
+      - ".flake8"
+  - label: "refactoring"
+    title:
+      - "/.* refactor.*/i"
+
+template: |
+  ## Changes
+
+  $CHANGES

CONTRIBUTING.rst

@@ -10,9 +10,9 @@ Bug reports/Feature Requests/Feedback/Questions
 It is incredibly helpful to us when users report bugs, unexpected behaviour, or request
 features. You can do the following:
 
-    * `Report a bug <https://github.com/steven-murray/21cmSense/issues/new?template=bug_report.md>`
-    * `Request a Feature <https://github.com/steven-murray/21cmSense/issues/new?template=feature_request.md>`
-    * `Ask a Question <https://github.com/steven-murray/21cmSense/issues/new?template=question.md>`
+    * `Report a bug <https://github.com/rasg-affiliates/21cmSense/issues/new?template=bug_report.md>`
+    * `Request a Feature <https://github.com/rasg-affiliates/21cmSense/issues/new?template=feature_request.md>`
+    * `Ask a Question <https://github.com/rasg-affiliates/21cmSense/issues/new?template=question.md>`
 
 When doing any of these, please try to be as succinct, but detailed, as possible, and use
 a "Minimum Working Example" whenever applicable.
@@ -32,7 +32,7 @@ pre-commit hooks will run that enforce the ``black`` coding style. If you do not
 install these requirements, you must manually run black before committing your changes,
 otherwise your changes will likely fail continuous integration.
 
-1. First fork `21cmSense <https://github.com/steven-murray/21cmSense>`_
+1. First fork `21cmSense <https://github.com/rasg-affiliates/21cmSense>`_
    (look for the "Fork" button), then clone the fork locally::
 
     git clone [email protected]:your_name_here/21cmSense.git

README.rst

@@ -2,15 +2,17 @@
 21cmSense
 =========
 
-.. image:: https://travis-ci.org/steven-murray/21cmSense.svg?branch=master
-    :target: https://travis-ci.org/steven-murray/21cmSense
-.. image:: https://codecov.io/gh/steven-murray/21cmSense/branch/master/graph/badge.svg
-  :target: https://codecov.io/gh/steven-murray/21cmSense
+.. image:: https://img.shields.io/pypi/pyversions/21cmSense
+   :alt: PyPI - Python Version
+.. image:: https://codecov.io/gh/rasg-affiliates/21cmSense/branch/main/graph/badge.svg
+    :target: https://codecov.io/gh/rasg-affiliates/21cmSense
 .. image:: https://img.shields.io/badge/code%20style-black-000000.svg
-  :target: https://github.com/psf/black
+    :target: https://github.com/psf/black
 .. image:: https://readthedocs.org/projects/21cmsense/badge/?version=latest
-  :target: https://21cmsense.readthedocs.io/en/latest/?badge=latest
-  :alt: Documentation Status
+    :target: https://21cmsense.readthedocs.io/en/latest/?badge=latest
+    :alt: Documentation Status
+.. image:: https://img.shields.io/github/license/Ileriayo/markdown-badges?style=flat
+    :target: ./LICENSE.rst
 
 A python package for calculating the expected sensitivities of 21cm experiments
 to the Epoch of Reionization and/or Cosmic Dawn power spectrum.

docs/conf.py

@@ -43,8 +43,8 @@
 
 pygments_style = "trac"
 extlinks = {
-    "issue": ("https://github.com/steven-murray/21cmSense/issues/%s", "#"),
-    "pr": ("https://github.com/steven-murray/21cmSense/pull/%s", "PR #"),
+    "issue": ("https://github.com/rasg-affiliates/21cmSense/issues/%s", "#"),
+    "pr": ("https://github.com/rasg-affiliates/21cmSense/pull/%s", "PR #"),
 }
 
 html_theme = "furo"

docs/tutorials/cli_tutorial.rst

@@ -13,13 +13,13 @@ files::
 
 These are all the configuration and data files we will need to perform the sensitivity
 estimate. You can obtain them
-`here <https://github.com/steven-murray/21cmSense/tree/main/docs/tutorials/data>`_.
+`here <https://github.com/rasg-affiliates/21cmSense/tree/main/docs/tutorials/data>`_.
 
 Antenna Positions
 ~~~~~~~~~~~~~~~~~
 In general you do not need a file of antenna positions -- you could alternatively specify
 a function to generate them (eg. see the default example
-`observatory config <https://github.com/steven-murray/21cmSense/blob/master/example_configs/observatory_hera.yml>`_).
+`observatory config <https://github.com/rasg-affiliates/21cmSense/blob/master/example_configs/observatory_hera.yml>`_).
 Typically, however, you will have a given list of positions. These can be in the format
 of a ``.npy`` array, a pickle file, or a simple ASCII file. In any case, the array must
 be of shape ``(Nant, 3)``, where the three columns are East, North and Elevation, all

py21cmsense/antpos.py

@@ -16,7 +16,7 @@
 
 @yaml.yaml_func()
 def hera(
-    hex_num,
+    hex_num: int,
     separation: tp.Length = 14 * un.m,
     split_core: bool = False,
     outriggers: bool = False,
@@ -46,6 +46,9 @@ def hera(
     antpos
         A 2D array of antenna positions, shape ``(Nants, 3)``.
     """
+    if hex_num <= 1:
+        raise ValueError("hex_num must be greater than 1")
+
     sep = separation.to_value("m")
 
     if row_separation is None:

py21cmsense/observatory.py

@@ -80,9 +80,14 @@ class Observatory:
     @_antpos.validator
     def _antpos_validator(self, att, val):
         tp.vld_physical_type("length")(self, att, val)
-        assert val.ndim == 2
-        assert val.shape[-1] == 3
-        assert val.shape[0] > 1
+        if val.ndim != 2:
+            raise ValueError("antpos must be a 2D array.")
+
+        if val.shape[-1] != 3:
+            raise ValueError("antpos must have shape (Nants, 3).")
+
+        if val.shape[0] <= 1:
+            raise ValueError("antpos must have at least two antennas.")
 
     @cached_property
     def antpos(self) -> np.ndarray:

setup.cfg

@@ -5,7 +5,7 @@ author = Jonathan Pober
 license = mit
 long_description = file: README.rst
 long_description_content_type = text/x-rst; charset=UTF-8
-url = https://github.com/steven-murray/21cmSense
+url = https://github.com/rasg-affiliates/21cmSense
 # Change if running only on Windows, Mac or Linux (comma-separated)
 platforms = any
 # Add here all kinds of additional classifiers as defined under

tests/test_antpos.py

@@ -6,7 +6,7 @@
 from py21cmsense.antpos import hera
 
 
-@pytest.mark.parametrize("n", [3, 5, 8, 1])
+@pytest.mark.parametrize("n", [3, 5, 8])
 def test_hera_split_core(n):
     # https://en.wikipedia.org/wiki/Centered_hexagonal_number
     # 3*n^2 - 3n + 1
@@ -16,7 +16,7 @@ def test_hera_split_core(n):
     assert len(antpos2) == len(antpos1) - n
 
 
-@pytest.mark.parametrize("n", [3, 5, 8, 1])
+@pytest.mark.parametrize("n", [3, 5, 8])
 def test_hera_outriggers(n):
     # https://en.wikipedia.org/wiki/Centered_hexagonal_number
     # 3*n^2 - 3n + 1
@@ -34,3 +34,8 @@ def test_hera_set_row_sep():
 
     antpos3 = hera(4, row_separation=12.12 * un.m)
     assert not np.allclose(antpos1, antpos3)
+
+
+def test_bad_hex_num():
+    with pytest.raises(ValueError):
+        hera(1)

tests/test_observatory.py

@@ -2,6 +2,7 @@
 
 import numpy as np
 import pyuvdata
+import re
 from astropy import units
 from astropy.coordinates import EarthLocation
 from pathlib import Path
@@ -28,9 +29,17 @@ def test_antpos(bm):
         Observatory(antpos=np.zeros((10, 3)) * units.s, beam=bm)
 
     # Need more than one antenna
-    with pytest.raises(AssertionError):
+    with pytest.raises(ValueError, match="antpos must have at least two antennas"):
         Observatory(antpos=np.zeros((1, 3)) * units.m, beam=bm)
 
+    with pytest.raises(ValueError, match="antpos must be a 2D array"):
+        Observatory(antpos=np.zeros(10) * units.m, beam=bm)
+
+    with pytest.raises(
+        ValueError, match=re.escape("antpos must have shape (Nants, 3)")
+    ):
+        Observatory(antpos=np.zeros((10, 2)) * units.m, beam=bm)
+
 
 def test_observatory_class(bm):
     a = Observatory(antpos=np.zeros((3, 3)) * units.m, beam=bm)