fixing linting and test helpers

README.md

@@ -1,15 +1,12 @@
-<a href="https://app.travis-ci.com/github/pirl-unc/mhcgnomes">
-    <img src="https://travis-ci.com/pirl-unc/mhcgnomes.svg?branch=main" alt="Build Status" />
-</a> 
+[![Tests](https://github.com/pirl-unc/mhcgnomes/actions/workflows/tests.yml/badge.svg)](https://github.com/pirl-unc/mhcgnomes/actions/workflows/tests.yml)
 <a href="https://coveralls.io/github/til-unc/mhcgnomes">
-    <img src="https://coveralls.io/repos/github/til-unc/mhcgnomes/badge.svg?branch=main" alt="Coverage Status">
+<img src="https://coveralls.io/repos/github/til-unc/mhcgnomes/badge.svg?branch=main" alt="Coverage Status">
 </a>
 <a href="https://pypi.python.org/pypi/mhcgnomes/">
-    <img src="https://img.shields.io/pypi/v/mhcgnomes.svg?maxAge=1000" alt="PyPI" />
+<img src="https://img.shields.io/pypi/v/mhcgnomes.svg?maxAge=1000" alt="PyPI" />
 </a>
 
-
-![](https://raw.githubusercontent.com/til-unc/mhcgnomes/main/gnome-red-text.png) 
+![](https://raw.githubusercontent.com/til-unc/mhcgnomes/main/gnome-red-text.png)
 
 # mhcgnomes: Parsing MHC nomenclature in the wild
 
@@ -23,10 +20,10 @@ aims to correctly parse every name in [IEDB](http://www.iedb.org/), [IMGT/HLA](h
 In [1]: mhcgnomes.parse("HLA-A0201")
 Out[1]: Allele(
     gene=Gene(
-        species=Species(name="Homo sapiens', prefix="HLA"), 
-        name="A"), 
-    allele_fields=("02", "01"), 
-    annotations=(), 
+        species=Species(name="Homo sapiens', prefix="HLA"),
+        name="A"),
+    allele_fields=("02", "01"),
+    annotations=(),
     mutations=())
 
 In [2]: mhcgnomes.parse("HLA-A0201").to_string()
@@ -43,40 +40,38 @@ Despite the valiant efforts of groups such as the [Comparative MHC Nomenclature
 
 For example, these all refer to the same MHC protein sequence:
 
-* "HLA-A\*02:01"
-* "HLA-A02:01"
-* "HLA-A:02:01"
-* "HLA-A0201"
-
+- "HLA-A\*02:01"
+- "HLA-A02:01"
+- "HLA-A:02:01"
+- "HLA-A0201"
 
 Additionally, for human alleles, the species prefix is often omitted:
 
-* "A\*02:01"
-* "A\*0201"
-* "A02:01"
-* "A:02:01"
-* "A0201"
-
+- "A\*02:01"
+- "A\*0201"
+- "A02:01"
+- "A:02:01"
+- "A0201"
 
 ### Annotations
 
-Sometimes, alleles are bundled with modifier suffixes which specify 
+Sometimes, alleles are bundled with modifier suffixes which specify
 the functionality or abundance of the MHC. Here's an example with an allele
 which is secreted instead of membrane-bound:
 
-* "HLA-A\*02:01:01S"
+- "HLA-A\*02:01:01S"
 
-These are collected in the `annotations` field of an 
+These are collected in the `annotations` field of an
 [`Allele`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/allele.py)
 result.
 
 ### Mutations
 
-MHC proteins are sometimes described in terms of mutations to a known allele. 
+MHC proteins are sometimes described in terms of mutations to a known allele.
 
-* "HLA-B\*08:01 N80I mutant"
+- "HLA-B\*08:01 N80I mutant"
 
-These mutations are collected in the `mutations` field of an 
+These mutations are collected in the `mutations` field of an
 [`Allele`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/allele.py) result.
 
 ### Beyond humans
@@ -85,78 +80,75 @@ To make things worse, several model organisms (like mice and rats) use archaic
 naming systems, where there is no notion of allele groups or four/six/eight
 digit alleles but every allele is simply given a name, such as:
 
-* "H2-Kk"
-* "RT1-9.5f"
-
+- "H2-Kk"
+- "RT1-9.5f"
 
 In the above example "H2"/"RT1" correspond to species, "K"/"9.5" are
 the gene names and "k"/"f" are the allele names.
 
-To make these even worse, the name of a species is subject to variation (e.g. "H2" vs. "H-2") as well as drift over time (e.g. ChLA -> MhcPatr -> Patr).  
+To make these even worse, the name of a species is subject to variation (e.g. "H2" vs. "H-2") as well as drift over time (e.g. ChLA -> MhcPatr -> Patr).
 
 ### Serotypes, haplotypes, and other named entitites
 
 Besides alleles are also other named MHC related entities you'll encounter in immunological data. Closely related to alleles are serotypes, which effectively denote a grouping of alleles that are all recognized by the same antibody:
 
-* "HLA-A2"
-* "A2"
+- "HLA-A2"
+- "A2"
 
-In many datasets the exact allele is not known but an experiment might note the genetic background of a model animal, resulting in loose haplotype restrictions such as: 
+In many datasets the exact allele is not known but an experiment might note the genetic background of a model animal, resulting in loose haplotype restrictions such as:
 
-* "H2-k class I"
+- "H2-k class I"
 
-Yes, good luck disambiguating "H2-k" the haplotype from "H2-K" the gene, especially since capitalization is not stable enough to be relied on for parsing. 
+Yes, good luck disambiguating "H2-k" the haplotype from "H2-K" the gene, especially since capitalization is not stable enough to be relied on for parsing.
 
-In some cases immunological data comes only with a denoted species (e.g. "mouse"), a gene (e.g. "HLA-A"), or an MHC class ("human class I"). MHCgnomes has a structured representation for all of these cases and more. 
+In some cases immunological data comes only with a denoted species (e.g. "mouse"), a gene (e.g. "HLA-A"), or an MHC class ("human class I"). MHCgnomes has a structured representation for all of these cases and more.
 
 ## Parsing strategy
 
-It is a fool's errand to curate *all* possible MHC allele names since that list grows daily as the MHC loci of more people (and non-human animals) are sequenced. Instead, MHCgnomes contains an ontology of curated species and genes and then attempts to parse any given string into a multiple candidates of the following types:
-
-* [`Species`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/species.py)
-* [`Gene`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/gene.py)
-* [`Allele`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/allele.py)
-* [`AlleleWithoutGene`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/allele_without_gene.py)
-* [`Class2Pair`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/class2_pair.py)
-* [`Class2Locus`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/class2_locus.py)
-* [`MhcClass`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/mhc_class.py)
-* [`Haplotype`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/haplotype.py)
-* [`Serotype`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/serotype.py)
-
-
-The set of candidate interpretations for each string are then 
-ranked according to heuristic rules. For example, a string will be 
-preferentially interpreted as an [`Allele`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/allele.py) rather 
+It is a fool's errand to curate _all_ possible MHC allele names since that list grows daily as the MHC loci of more people (and non-human animals) are sequenced. Instead, MHCgnomes contains an ontology of curated species and genes and then attempts to parse any given string into a multiple candidates of the following types:
+
+- [`Species`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/species.py)
+- [`Gene`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/gene.py)
+- [`Allele`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/allele.py)
+- [`AlleleWithoutGene`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/allele_without_gene.py)
+- [`Class2Pair`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/class2_pair.py)
+- [`Class2Locus`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/class2_locus.py)
+- [`MhcClass`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/mhc_class.py)
+- [`Haplotype`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/haplotype.py)
+- [`Serotype`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/serotype.py)
+
+The set of candidate interpretations for each string are then
+ranked according to heuristic rules. For example, a string will be
+preferentially interpreted as an [`Allele`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/allele.py) rather
 than a [`Serotype`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/serotype.py)
-or [`Haplotype`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/haplotype.py). 
-
+or [`Haplotype`](https://github.com/til-unc/mhcgnomes/blob/main/mhcgnomes/haplotype.py).
 
 ## How many digits per field?
 
 Originally alleles for many genes were numbered with two digits:
 
-* "HLA-MICB\*01"
+- "HLA-MICB\*01"
 
 But as the number of identified alleles increased, the number of
-fields specifying a distinct protein increase to two. This became 
+fields specifying a distinct protein increase to two. This became
 conventionally called a "four digit" format, since each field has two
-digits. Yet, as the number of identified alleles continued to increase, then 
-the number of digits per field has often increased from two to three: 
+digits. Yet, as the number of identified alleles continued to increase, then
+the number of digits per field has often increased from two to three:
 
-* "MICB\*002:01"
-* "HLA-A00201"
-* "A:002:01"
-* "A\*00201"
+- "MICB\*002:01"
+- "HLA-A00201"
+- "A:002:01"
+- "A\*00201"
 
 These are not always currently treated as equivalent to allele strings with two digits in their first field, but that feature is in the works.
 
-However, if databases such as [IPD-MHC](https://www.ebi.ac.uk/ipd/mhc/) or [IMGT-HLA](https://www.ebi.ac.uk/ipd/imgt/hla/) recorded an older form of an allele, then MHCgnomes can optionally map it onto the modern version (including capturing differences in numbers of digits per field). 
+However, if databases such as [IPD-MHC](https://www.ebi.ac.uk/ipd/mhc/) or [IMGT-HLA](https://www.ebi.ac.uk/ipd/imgt/hla/) recorded an older form of an allele, then MHCgnomes can optionally map it onto the modern version (including capturing differences in numbers of digits per field).
 
 ## References
 
-* [IPD-MHC: nomenclature requirements for the non-human major histocompatibility complex in the next-generation sequencing era](https://link.springer.com/article/10.1007%2Fs00251-018-1072-4)
-* [Comparative MHC nomenclature: report from the ISAG/IUIS-VIC committee 2018]()
-* [ISAG/IUIS-VIC Comparative MHC Nomenclature
-Committee report, 2005](https://link.springer.com/content/pdf/10.1007%2Fs00251-005-0071-4.pdf)
-* [Marsupial MHC Class II β Genes Are Not Orthologous to the Eutherian β Gene Families]()
-* [Nomenclature for factors of the SLA system, update 2008](https://www.ncbi.nlm.nih.gov/pubmed/19317739)
+- [IPD-MHC: nomenclature requirements for the non-human major histocompatibility complex in the next-generation sequencing era](https://link.springer.com/article/10.1007%2Fs00251-018-1072-4)
+- [Comparative MHC nomenclature: report from the ISAG/IUIS-VIC committee 2018]()
+- [ISAG/IUIS-VIC Comparative MHC Nomenclature
+  Committee report, 2005](https://link.springer.com/content/pdf/10.1007%2Fs00251-005-0071-4.pdf)
+- [Marsupial MHC Class II β Genes Are Not Orthologous to the Eutherian β Gene Families]()
+- [Nomenclature for factors of the SLA system, update 2008](https://www.ncbi.nlm.nih.gov/pubmed/19317739)

lint.sh

@@ -7,7 +7,7 @@ set -o errexit
 # - https://bitbucket.org/logilab/pylint/issues/701/false-positives-with-not-an-iterable-and
 # - https://bitbucket.org/logilab/pylint/issues/58
 
-find mhcgnomes test -name '*.py' \
+find mhcgnomes tests -name '*.py' \
   | xargs pylint \
   --errors-only \
   --disable=unsubscriptable-object,not-an-iterable,no-member

mhcgnomes/dataframe.py

@@ -12,7 +12,6 @@
 
 import pandas as pd
 
-from .function_api import parse
 
 def dataframe_from_parsed_objects(parsed_objects):
     records = [
@@ -23,5 +22,7 @@ def dataframe_from_parsed_objects(parsed_objects):
 
 
 def dataframe_from_string_list(names):
+    from .function_api import parse
+
     parsed_objects = [parse(name) for name in names]
     return dataframe_from_parsed_objects(parsed_objects)

mhcgnomes/function_api.py

@@ -11,8 +11,8 @@
 # limitations under the License.
 
 from .common import cache
-from .parser import Parser
 from .parser import (
+    Parser,
     DEFAULT_SPECIES_PREFIX,
     USE_ALLELE_ALIASES,
     GENE_SEPS,

tests/common.py

@@ -10,6 +10,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from functools import wraps
+
 def ok_(a, s=None):
     if s is None:
         assert a
@@ -56,4 +58,30 @@ def almost_eq_(a, b, tol=1e-6, s=None):
     if s is None:
         assert abs(a - b) < tol
     else:
-        assert abs(a - b) < tol, s
+        assert abs(a - b) < tol, s
+
+class assert_raises:
+    def __init__(self, *exception_types):
+        self.exception_types = exception_types
+
+    def __enter__(self):
+        pass
+
+    def to_string(self):
+        return " or ".join(["%s" % e for e in self.exception_types])
+
+    def __exit__(self, type, value, traceback):
+        if type is None:
+            raise AssertionError("Expected exception %s not raised" % self.to_string())
+        if type not in self.exception_types:
+            raise AssertionError("Expected exception %s, got %s" % (self.to_string(), type))
+        return True
+
+def raises(*exception_types):
+    def decorator(f):
+        @wraps(f)
+        def wrapper(*args, **kwargs):
+            with assert_raises(*exception_types):
+                f(*args, **kwargs)
+        return wrapper
+    return decorator