poly->dnadesign (#7)

* update poly->dnadesign * remove blocking issues
Koeng101 · Dec 10, 2023 · c57660d · c57660d
1 parent e8a10e3
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diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -1,6 +1,6 @@
 // For format details, see https://aka.ms/devcontainer.json.
 {
-	"name": "poly-devcontainer",
+	"name": "dnadesign-devcontainer",
 	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
 	"image": "mcr.microsoft.com/devcontainers/base:bullseye",
 
@@ -27,4 +27,4 @@
 
 	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
 	// "remoteUser": "root"
-}
+}
diff --git a/.github/FUNDING.yml b/.github/FUNDING.yml
@@ -1,6 +1,6 @@
 # These are supported funding model platforms
 
-github: [TimothyStiles]
+github: #[koeng101]
 patreon: # Replace with a single Patreon username
 open_collective: # Replace with a single Open Collective username
 ko_fi: # Replace with a single Ko-fi username

diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -1,6 +1,6 @@
 ---
 name: Bug report
-about: Is something broken? Create a bug report to help us improve `poly`! No issue is too small :)
+about: Is something broken? Create a bug report to help us improve `dnadesign`! No issue is too small :)
 title: ''
 labels: ['needs-triage', 'bug']
 assignees: ''
@@ -33,4 +33,4 @@ limited capacity and will prioritize more severe bugs!*
 *This is very important, so please fill it out!*
  - OS: [e.g. `Fedora 36`, `Ubuntu 22.04`, `Windows 11`, etc.]
  - Golang version: [e.g. `1.21`]
- - `poly` version [e.g. `v0.23`]
+ - `dnadesign` version [e.g. `v0.23`]
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
@@ -1,6 +1,6 @@
 ---
 name: Feature request
-about: Do you wish poly had a specific feature? Do you have ideas for improvements to the current API? Do you feel like documentation for a feature needs expansion? Big or small, we appreciate your feedback!
+about: Do you wish dnadesign had a specific feature? Do you have ideas for improvements to the current API? Do you feel like documentation for a feature needs expansion? Big or small, we appreciate your feedback!
 title: ''
 labels: ['needs-triage', 'enhancement']
 assignees: ''

diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -5,7 +5,7 @@
 *Explain why these changes are necessary. Link to GitHub issues here with the format `fixes: #XXX` to indicate this PR resolves the issue.*
 
 ### Are any changes breaking? (IMPORTANT)
-*Will merging this PR change `poly`'s API in a non-backwards-compatible manner?*
+*Will merging this PR change `dnadesign`'s API in a non-backwards-compatible manner?*
 
 *Examples of breaking changes:*
 * *Removing a method from a struct.*

diff --git a/.github/workflows/blocking_issues.yml b/.github/workflows/blocking_issues.yml
diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
@@ -24,8 +24,8 @@ jobs:
         uses: schneegans/dynamic-badges-action@master
         with:
           auth: ${{ secrets.COVERAGE_GIST}}
-          gistID: e58f265655ac0acacdd1a38376ccd32a
+          gistID: e8462880f920d70b182d5df3617b30f5
           filename: coverage.json
           label: Coverage
           message: ${{ env.COVERAGE }}
-          color: green
+          color: green
diff --git a/.github/workflows/notify.yml b/.github/workflows/notify.yml
diff --git a/.gitpod.Dockerfile b/.gitpod.Dockerfile
diff --git a/.gitpod.yml b/.gitpod.yml
diff --git a/.goreleaser.yml b/.goreleaser.yml
@@ -14,8 +14,8 @@ release:
   # Default is extracted from the origin remote URL or empty if its private hosted.
   # Note: it can only be one: either github or gitlab or gitea
   github:
-    owner: timothystiles
-    name: poly
+    owner: koeng101
+    name: dnadesign
 
   # IDs of the archives to use.
   # Defaults to all.
@@ -40,4 +40,4 @@ release:
   # You can disable this pipe in order to not upload any artifacts to
   # GitHub.
   # Defaults to false.
-  # disable: true
+  # disable: true
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -1,3 +1,3 @@
 {
-	"cSpell.words": ["bioinformatics", "genbank", "polyjson"]
+	"cSpell.words": ["bioinformatics", "genbank"]
 }
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,35 +6,3 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
-
-### Added
-- Alternative start codons can now be used in the `synthesis/codon` DNA -> protein translation package (#305)
-- Added a parser and writer for the `pileup` sequence alignment format (#329)
-- Added statistics to the `synthesis/codon` package (keeping track of the observed start codon occurrences in a translation table) (#350)
-- Added option to fragmenter to fragment with only certain overhangs (#387)
-- GoldenGates with methylated sequences using lowercase letters (#391)
-- Generic parser is now implemented across all parsers for consistent interactions. [(#339)](https://github.com/koeng101/dnadesign/issues/339)
-- Alternative start codons can now be used in the `synthesis/codon` DNA -> protein translation package [(#305)](https://github.com/koeng101/dnadesign/issues/305)
-- Added a parser and writer for the `pileup` sequence alignment format [(#329)](https://github.com/koeng101/dnadesign/issues/329)
-- Created copy methods for Feature and Location to address concerns raised by [(#342)](https://github.com/koeng101/dnadesign/issues/342)
-- Created new methods to convert polyjson -> genbank.
-- Created new `Feature.StoreSequence` method to enable [(#388)](https://github.com/koeng101/dnadesign/issues/388)
-- Added seqhash v2 (#398)
-
-### Changed
-- **Breaking**: Genbank parser uses new custom multimap for `Feature.Attributes`, which allows for duplicate keys. This changes the type of Features.Attributes from `map[string]string` to `MultiMap[string, string]`, an alias for `map[string]string` defined in `multimap.go`. [(#383)](https://github.com/koeng101/dnadesign/issues/383)
-- Improves error reporting for genbank parse errors via a new `ParseError` struct.
-
-### Fixed
-- `fastq` parser no longer becomes de-aligned when reading [(#325)](https://github.com/koeng101/dnadesign/issues/325)
-- `fastq` now handles optionals correctly [(#323)](https://github.com/koeng101/dnadesign/issues/323)
-- Adds functional test and fix for [(#313)](https://github.com/koeng101/dnadesign/issues/313).
-- In addition to expanding the set of genbank files which can be validly parsed, the parser is more vocal when it encounters unusual syntax in the "feature" section. This "fail fast" approach is better as there were cases where inputs triggered a codepath which would neither return a valid Genbank object nor an error, and should help with debugging.
--  Fixed bug that produced wrong overhang in linear, non-directional, single cut reactions. #408
->>>>>>> main
-
-## [0.26.0] - 2023-07-22
-Oops, we weren't keeping a changelog before this tag!
-
-[unreleased]: https://github.com/koeng101/dnadesign/compare/v0.26.0...main
-[0.26.0]: https://github.com/koeng101/dnadesign/releases/tag/v0.26.0
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
-All copyright for portions of Poly prior to commit f76bf05 are held by Timothy
-Stiles, 2023 as part of project Poly. All other copyright for Poly are held by
-Keoni Gandall, 2023.
+All copyright for portions of DnaDesign prior to commit f76bf05 are held by
+Timothy Stiles, 2023 as part of project Poly. All other copyright for
+DnaDesign are held by Keoni Gandall, 2023.
 
 Copyright (c) 2023 Keoni Gandall