overhaul project

.github/ISSUE_TEMPLATE/bug.yaml

@@ -0,0 +1,46 @@
+# SPDX-FileCopyrightText: Copyright 2020-2023, Contributors to CICD
+# SPDX-PackageHomePage: https://github.com/dmyersturnbull/cicd
+# SPDX-License-Identifier: Apache-2.0
+
+name: "🐛 Bug"
+description: "Bug report"
+labels: ["type: fix"]
+
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: What happened?
+      placeholder: Detail what you did and what happened.
+    validations:
+      required: true
+  - type: dropdown
+    id: os
+    attributes:
+      label: What OS types are you seeing the problem on?
+      multiple: true
+      options:
+        - Windows
+        - Linux
+        - macOS
+    validations:
+      required: false
+  - type: dropdown
+    id: browsers
+    attributes:
+      label: What browsers are you seeing the problem on?
+      multiple: true
+      options:
+        - Chrome
+        - Firefox
+        - Edge
+        - Safari
+        - Opera
+        - Samsung Internet
+    validations:
+      required: false
+  - type: textarea
+    id: logs
+    attributes:
+      label: Relevant log output
+      description: Please copy and paste any relevant log output.

.github/ISSUE_TEMPLATE/docs.yaml

@@ -0,0 +1,16 @@
+# SPDX-FileCopyrightText: Copyright 2020-2023, Contributors to CICD
+# SPDX-PackageHomePage: https://github.com/dmyersturnbull/cicd
+# SPDX-License-Identifier: Apache-2.0
+
+name: "📚 Documentation"
+description: "Documentation issue"
+labels: ["type: docs"]
+
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: What needs work?
+      placeholder: Describe the documentation issue.
+    validations:
+      required: true

.github/ISSUE_TEMPLATE/feature.yaml

@@ -0,0 +1,16 @@
+# SPDX-FileCopyrightText: Copyright 2020-2023, Contributors to CICD
+# SPDX-PackageHomePage: https://github.com/dmyersturnbull/cicd
+# SPDX-License-Identifier: Apache-2.0
+
+name: "✨ Feature"
+description: "Feature request"
+labels: ["type: feature"]
+
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: What is the feature request?
+      placeholder: Describe the feature you would like.
+    validations:
+      required: true

.github/ISSUE_TEMPLATE/performance.yaml

@@ -0,0 +1,51 @@
+# SPDX-FileCopyrightText: Copyright 2020-2023, Contributors to CICD
+# SPDX-PackageHomePage: https://github.com/dmyersturnbull/cicd
+# SPDX-License-Identifier: Apache-2.0
+
+name: "🐢 Performance"
+description: "Performance issue"
+labels: ["type: performance"]
+
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: What is the performance issue?
+      placeholder: Detail your steps and where the performance dropped.
+    validations:
+      required: true
+  - type: input
+    id: version
+    attributes:
+      label: Version
+      description: What version are you running?
+  - type: dropdown
+    id: os
+    attributes:
+      label: What OS types are you seeing the problem on?
+      multiple: true
+      options:
+        - Windows
+        - Linux
+        - macOS
+    validations:
+      required: false
+  - type: dropdown
+    id: browsers
+    attributes:
+      label: What browsers are you seeing the problem on?
+      multiple: true
+      options:
+        - Chrome
+        - Firefox
+        - Edge
+        - Safari
+        - Opera
+        - Samsung Internet
+    validations:
+      required: false
+  - type: textarea
+    id: logs
+    attributes:
+      label: Relevant log output
+      description: Please copy and paste any relevant log output.

.github/PULL_REQUEST_TEMPLATE/pull_request.md

@@ -0,0 +1 @@
+# Pull request

.github/workflows/build.yaml

@@ -0,0 +1,43 @@
+# This workflow will build a Java project with Gradle
+# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-gradle
+
+name: Test
+
+on:
+  workflow_call:
+    inputs:
+      ref:
+        type: string
+        description: Ref to checkout
+        default: main
+
+permissions:
+  contents: read
+  statuses: read
+  actions: read
+  security-events: write
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up JDK 20
+        uses: actions/setup-java@v2
+        with:
+          distribution: oracle
+          java-version: "21-ea"
+      - uses: gradle/wrapper-validation-action@v1
+      - name: Set up and execute Gradle test
+        uses: gradle/gradle-build-action@v2
+        with:
+          arguments: test
+      - uses: actions/upload-artifact@v3
+        with:
+          name: package
+          path: build/libs
+      - uses: actions/upload-artifact@v3
+        with:
+          name: build-reports
+          path: build/reports/

.github/workflows/checks.yaml

@@ -0,0 +1,30 @@
+# Various static code analysis and checks
+# Runs on commit or pull (to any branch)
+# and on a schedule (weekly)
+name: Static checks
+on:
+  push:
+  pull_request:
+  schedule:
+    - cron: 0 7 * * 6
+jobs:
+  markdown-link-check:
+    name: Check Markdown links
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@master
+      - uses: gaurav-nelson/github-action-markdown-link-check@v1
+  analyse:
+    name: Analyze with CodeQL
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 2
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v1
+      - name: Autobuild with CodeQL
+        uses: github/codeql-action/autobuild@v1
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v1

.gitignore

@@ -37,6 +37,9 @@ Gemfile.lock
 # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
 hs_err_pid*
 
+# IDE files
+.idea
+
 # Keep these config files
 !/.gitignore
 !/.travis.yml

README.md

@@ -3,26 +3,34 @@
 ![stability-stable](https://img.shields.io/badge/stability-stable-green.svg)
 ![Active](https://img.shields.io/static/v1?label=development&message=active&color=green)
 [![License](https://img.shields.io/badge/license-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
-![Latest release](https://img.shields.io/github/v/tag/dmyersturnbull/genomics-io)
+![Latest release](https://img.shields.io/github/v/tag/dmyersturnbull/bioio)
 ![Java compatibility](https://img.shields.io/static/v1?label=Java&message=14%2b)
-![Maven Central](https://img.shields.io/maven-central/v/dmyersturnbull/genomics-io)
-![GitHub last commit](https://img.shields.io/github/last-commit/dmyersturnbull/genomics-io?color=green)
+![Maven Central](https://img.shields.io/maven-central/v/dmyersturnbull/bioio)
+![GitHub last commit](https://img.shields.io/github/last-commit/dmyersturnbull/bioio?color=green)
 
 Efficient, high-quality streaming parsers and writers for 12 text-based formats used in bioinformatics.
 
 The goal is to have the best possible parsers for the most problematic ancient formats.
 
 **Supported formats:**
-VCF, FASTA, GenBank, BED, GFF/GTV/GVF, UCSC chain,
-pre-MAKEPED, BGEE, Turtle/RDF,
-matrices/tables/CSV/TSV
+
+- Variant calls: VCF
+- Gene features: GenBank, BED, GFF3, GTF, GVF
+- Sequences: FASTA, FASTA alignment, FASTQ
+- Expression: BGEE
+- Coordinate mapping: UCSC chain
+- Phylogenetics/pedigree: pre-MAKEPED
+- Protein structure: PDB
+- Triples: Turtle, RDF
+- Tabular: CSV, TSV, etc.
 
 **Features & choices:**
 
 - Reads and writes Java 8+ Streams, keeping only essential metadata in memory.
 - Parses every part of a format, leaving nothing as text unnecessarily.
 - Has a consistent API. Coordinates are always 0-indexed and text is always escaped (according to specifications).
 - Immutable, thread-safe, null-pointer-safe (`Optional<>`), and arbitrary-precision.
+- All methods are either exposed through interfaces, or reside in records, enums, and final classes
 
 #### Example:
 
@@ -33,7 +41,7 @@ import org.pharmgkb.parsers.vcf;
 
 Stream<VcfPosition> goodMitochondrialCalls = new VcfDataParser().parseFile(path)
 	.filter(p -> p.chromosome.isMitochondial())
-	.filter(VcfFilters.qualityAtLeast(10)) // converts to BigDecimal
+	.filter(VcfFilters.qualityAtLeast(10)); // converts to BigDecimal
 
 new VcfDataWriter().writeToFile(goodMitochondrialCalls, filteredPath);
 ```
@@ -67,7 +75,7 @@ implementation group: 'com.pharmgkb.bioio', name: 'bioio', version: '0.3.0'
 
 #### Pre-build JAR
 
-[Releases](https://github.com/dmyersturnbull/genomics-io/releases) contain both _fat_ JARs (containing dependencies)
+[Releases](https://github.com/dmyersturnbull/bioio/releases) contain both _fat_ JARs (containing dependencies)
 and _thin_ JARs (without dependencies), independently for each subproject
 (e.g. `bioio-vcf` for VCF, or `bioio-gff` for GFF/GTV/GVF).
 
@@ -84,7 +92,7 @@ Formats listed in bold are currently implemented.
 
 - Variant calls: **VCF**
 - Gene features: **GenBank, BED, GFF3, GTF, GVF**
-- Sequences: **FASTA**, EMBL, FASTA alignment, **FASTQ**, Seq, faidx (FASTQ indices)
+- Sequences: **FASTA**, EMBL, **FASTA alignment**, **FASTQ**, Seq, faidx (FASTQ indices)
 - Expression: **BGEE**
 - Coordinate mapping: **UCSC chain**
 - Phylogenetics & pedigrees: **pre-MAKEPED**, LINKAGE, Nexus
@@ -93,7 +101,7 @@ Formats listed in bold are currently implemented.
 - Protein structure: PDB (non-comprehensive)
 - RNA structure: Bpseq, Connect/CT, Vienna, Base-Paring, Dot-Bracket, Dot-Plot
 - Other: cytoband
-- Misc: Matrices/tables/CSV/TSV, alignment, **Turtle (and RDF)**
+- Misc: **Matrices/tables/CSV/TSV**, **Turtle (and RDF)**
 
 ### Extra things
 
@@ -220,17 +228,17 @@ List<AlignmentResult> topScores = parser.parseAll(Files.lines(fastaFile))
 ```java
 // Stream Triples in Turtle format from a URL
 /*
-@prefix myPrefix: <http://abc#owner> .
-<http://abc#cat> "belongsTo" @myPrefix ;
-	"hasSynonym" <http://abc#feline> .
+@prefix myPrefix: <https://abc#owner> .
+<https://abc#cat> "belongsTo" @myPrefix ;
+	"hasSynonym" <https://abc#feline> .
  */
 Stream<String> input = null;
 try (BufferedReader reader = new BufferedReader(new InputStreamReader((HttpURLConnection) myUrl.openConnection()).getInputStream()))) {
 	input = reader.lines();
 }
 TripleParser parser = new TripleParser(true);  // usePrefixes=true will replace prefixes
 Stream<Triple> stream = input.map(new TripleParser());
-// contains:  List[ http://abc#cat belongsTo http://abc#owner , http://abc#cat hasSynonym http://abc#feline ]
+// contains:  List[ https://abc#cat belongsTo https://abc#owner , https://abc#cat hasSynonym https://abc#feline ]
 List<Prefix> prefixes = parser.getPrefixes();
 ```
 
@@ -257,18 +265,18 @@ Map<String, Long> genotypeCounts = new VcfDataParser().parseAll(input)
 ```
 
 ```java
-Stream<BigDecimal> MatrixParser.tabs().parseAll(file).map(BigDecimal::new);
+Stream<BigDecimal> org.pharmgkb.parsers.text.MatrixParserI.tabs().parseAll(file).map(BigDecimal::new);
 ```
 
 ### Guiding principles
 
 1. Where possible, a parser is a `Function<String, R>` or `Function<Stream<String>, R>`,
    and writer is a `Function<R, String>` or `Function<R, Stream<String>>`.
-   [Java 8+ Streams](http://www.oracle.com/technetwork/articles/java/ma14-java-se-8-streams-2177646.html)
+   [Java 8+ Streams](https://www.oracle.com/technetwork/articles/java/ma14-java-se-8-streams-2177646.html)
    are expected to be used.
 2. Null values are generally banned from public methods in favor of
    [`Optional`](https://download.java.net/java/early_access/jdk16/docs/api/java.base/java/util/Optional.html).
-   See http://www.oracle.com/technetwork/articles/java/java8-optional-2175753.html for more information.
+   See https://www.oracle.com/technetwork/articles/java/java8-optional-2175753.html for more information.
 3. Most operations are thread-safe. Thread safety is annotated using `javax.annotation.concurrent`.
 4. Top-level data classes are immutable, as annotated by or `javax.annotation.concurrent.Immutable`.
 5. The builder pattern is used for non-trivial classes. Each builder has a copy constructor.

bed/build.gradle

@@ -1,3 +1,3 @@
 dependencies {
-	compile project(':core')
-}
+    api project(':core')
+}

bed/src/main/java/org/pharmgkb/parsers/bed/BedParser.java

@@ -1,7 +1,6 @@
 package org.pharmgkb.parsers.bed;
 
 import org.pharmgkb.parsers.BadDataFormatException;
-import org.pharmgkb.parsers.LineParser;
 import org.pharmgkb.parsers.bed.model.BedFeature;
 import org.pharmgkb.parsers.model.Strand;
 import org.slf4j.Logger;
@@ -42,18 +41,18 @@
  *
  * @author Douglas Myers-Turnbull
  * @see BedFeature
- * @see org.pharmgkb.parsers.bed.BedWriter
+ * @see BedWriter
  */
 @ThreadSafe
-public class BedParser implements LineParser<BedFeature> {
+public class BedParser implements BedParserI {
 
 	private static final long sf_logEvery = 10000;
 	private static final Pattern sf_comma = Pattern.compile(",");
 	private static final Pattern sf_tab = Pattern.compile("\t");
 
 	private static final Logger sf_logger = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
 
-	private AtomicLong m_lineNumber = new AtomicLong(0L);
+	private final AtomicLong m_lineNumber = new AtomicLong(0L);
 
 	@Nonnull
 	@Override
@@ -81,7 +80,7 @@ public BedFeature apply(@Nonnull String line) throws BadDataFormatException {
 				builder.setScore(Integer.parseInt(parts[4]));
 			}
 			if (parts.length > 5) {
-				builder.setStrand(Strand.lookupBySymbol(parts[5]));
+				builder.setStrand(Strand.fromSymbol(parts[5]));
 			}
 			if (parts.length > 6) {
 				builder.setThickStart(Long.parseLong(parts[6]));

bed/src/main/java/org/pharmgkb/parsers/bed/BedParserI.java

@@ -0,0 +1,8 @@
+package org.pharmgkb.parsers.bed;
+
+import org.pharmgkb.parsers.LineParser;
+import org.pharmgkb.parsers.bed.model.BedFeature;
+
+public interface BedParserI extends LineParser<BedFeature> {
+
+}