Added slow5 parser

.github/workflows/coverage.yml

@@ -3,7 +3,7 @@ name: Build Coverage Badge
 on:
   push:
     branches:
-      - prime
+      - main
 
 jobs:
   coverage-badge:

.github/workflows/golangci-lint.yml

@@ -1,10 +1,11 @@
 name: golangci-lint
+
 on:
   push:
     tags:
       - v*
     branches:
-      - prime
+      - main
   pull_request:
 jobs:
   golangci:

.github/workflows/notify.yml

@@ -2,18 +2,14 @@ name: notify social media
 
 on:
   release: 
-  issues: 
-  pull_request:
-  issue_comment: 
-  pull_request_review:
-  pull_request_review_comment: 
+  issues:
+  issue_comment:
   discussion: 
   discussion_comment:
   push:
     branches:
       - notify # for testing purposes
       - dev
-      - prime
       - main
 
 jobs:
@@ -24,4 +20,4 @@ jobs:
       - name: Actions for Discord
         env:
           DISCORD_WEBHOOK: ${{ secrets.DISCORD_WEBHOOK }}
-        uses: Ilshidur/action-discord@0.3.2
+        uses: Ilshidur/action-discord@0.3.2

.github/workflows/release.yml

@@ -18,12 +18,12 @@ jobs:
         name: Set up Go
         uses: actions/setup-go@v2
         with:
-          go-version: 1.16
+          go-version: 1.18
       -
         name: Run GoReleaser
         uses: goreleaser/goreleaser-action@v2
         with:
           version: latest
           args: release --rm-dist
         env:
-          GITHUB_TOKEN: ${{ secrets.HOMEBREW_DEPLOY_SECRET }}
+          GITHUB_TOKEN: ${{ secrets.HOMEBREW_DEPLOY_SECRET }}

.github/workflows/test.yml

@@ -3,7 +3,7 @@ on:
     tags:
       - v*
     branches:
-      - prime
+      - main
   pull_request:
 name: Test
 jobs:

.github/workflows/tweet.yml

@@ -0,0 +1,25 @@
+name: tweet
+
+on:
+  release:
+  issues: 
+    types: [opened]
+  push:
+    branches:
+      - notify # for testing purposes
+      - main
+      - dev
+
+jobs:
+  tweet:
+    runs-on: ubuntu-latest
+    steps:
+      - name: debug
+        uses: hmarr/debug-action@v2
+      - name: post event url to twitter
+        uses: TimothyStiles/Github-Twittction@v1.0.3
+        with:
+            twitter_consumer_key: ${{ secrets.TWITTER_CONSUMER_API_KEY }} 
+            twitter_consumer_secret: ${{ secrets.TWITTER_CONSUMER_API_SECRET }} 
+            twitter_access_token_key: ${{ secrets.TWITTER_ACCESS_TOKEN }} 
+            twitter_access_token_secret: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}

.gitignore

@@ -1,3 +1,5 @@
+# Test  files
+io/fasta/data/uniprot_1mb_test.fasta
 data/genbank
 public
 *.scratch
@@ -92,6 +94,7 @@ flycheck_*.el
 # Test binary, built with `go test -c`
 *.test
 
+
 # Output of the go coverage tool, specifically when used with LiteIDE
 *.out
 

.gitpod.Dockerfile

@@ -0,0 +1,14 @@
+# You can find the new timestamped tags here: https://hub.docker.com/r/gitpod/workspace-base/tags
+FROM gitpod/workspace-base:2022-04-26-07-40-59
+
+# Change your version here
+ENV GO_VERSION=1.18
+
+# For ref, see: https://github.com/gitpod-io/workspace-images/blob/61df77aad71689504112e1087bb7e26d45a43d10/chunks/lang-go/Dockerfile#L10
+ENV GOPATH=$HOME/go-packages
+ENV GOROOT=$HOME/go
+ENV PATH=$GOROOT/bin:$GOPATH/bin:$PATH
+RUN curl -fsSL https://dl.google.com/go/go${GO_VERSION}.linux-amd64.tar.gz | tar xzs \
+    && printf '%s\n' 'export GOPATH=/workspace/go' \
+                      'export PATH=$GOPATH/bin:$PATH' > $HOME/.bashrc.d/300-go
+

.gitpod.yml

@@ -0,0 +1,47 @@
+# This configuration file was automatically generated by Gitpod.
+# Please adjust to your needs (see https://www.gitpod.io/docs/config-gitpod-file)
+# and commit this file to your remote git repository to share the goodness with others.
+
+tasks:
+  - name: Golang
+    init: >
+     go get && 
+     go build ./... && 
+     go test ./...
+
+  # https://github.com/golang/vscode-go/wiki/tools
+  - name: Install Go Analysis Tools
+    init: |
+      go install -v github.com/cweill/gotests/gotests@latest
+      go install -v github.com/fatih/gomodifytags@latest
+      go install -v github.com/go-delve/delve/cmd/dlv@latest
+      go install -v github.com/haya14busa/goplay/cmd/goplay@latest
+      go install -v github.com/josharian/impl@latest
+      go install -v github.com/ramya-rao-a/go-outline@latest
+      go install -v github.com/rogpeppe/godef@latest
+      go install -v golang.org/x/tools/gopls@latest
+      go install -v honnef.co/go/tools/cmd/staticcheck@latest
+      clear
+
+  - name: Open Tutorial Readme   
+    command: >
+      gp ports await 23000 &&
+      clear &&
+      if [ -n "$tutorial" ]; then gp open tutorials/README.md && clear; fi
+
+image:
+  file: .gitpod.Dockerfile
+
+github:
+  prebuilds:
+    master: true
+    branches: true
+    pullRequests: true
+    pullRequestsFromForks: true
+    addCheck: false
+    addComment: true
+    addBadge: false
+
+vscode:
+  extensions:
+    - golang.go

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2022 Timothy Stiles
+Copyright (c) 2023 Timothy Stiles
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,7 +1,7 @@
 # (Poly)merase <img align="right" src="https://cdn.discordapp.com/attachments/766785755305213953/777596834734145546/ProfileFrameArtboard_1.png" width="100">
 
 [![PkgGoDev](https://pkg.go.dev/badge/github.com/TimothyStiles/poly)](https://pkg.go.dev/github.com/TimothyStiles/poly)
-[![GitHub license](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/TimothyStiles/poly/blob/prime/LICENSE) 
+[![GitHub license](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/TimothyStiles/poly/blob/main/LICENSE) 
 ![Tests](https://github.com/TimothyStiles/poly/workflows/Test/badge.svg)
 ![Test Coverage](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/TimothyStiles/e58f265655ac0acacdd1a38376ccd32a/raw/coverage.json)
 
@@ -18,9 +18,10 @@ Poly is a Go package for engineering organisms.
 
 ## Install
 
-`go install github.com/TimothyStiles/poly`
+`go get github.com/TimothyStiles/poly@latest`
 
 ## Documentation
+* **[Tutorials](https://gitpod.io/#tutorial=true/https://github.com/TimothyStiles/poly)**
 
 * **[Library](https://pkg.go.dev/github.com/TimothyStiles/poly#pkg-examples)**
 
@@ -44,4 +45,4 @@ Poly is a Go package for engineering organisms.
 
 * [MIT](LICENSE)
 
-* Copyright (c) 2022 Timothy Stiles
+* Copyright (c) 2023 Timothy Stiles