{"action":"created","issue":{"url":"https://api.github.com/repos/steinbaugh/basejump/issues/54","repository_url":"https://api.github.com/repos/steinbaugh/basejump","labels_url":"https://api.github.com/repos/steinbaugh/basejump/issues/54/labels{/name}","comments_url":"https://api.github.com/repos/steinbaugh/basejump/issues/54/comments","events_url":"https://api.github.com/repos/steinbaugh/basejump/issues/54/events","html_url":"https://github.com/steinbaugh/basejump/pull/54","id":270631452,"number":54,"title":"0.1.1 additional updates","user":{"login":"mjsteinbaugh","id":1760218,"avatar_url":"https://avatars1.githubusercontent.com/u/1760218?v=4","gravatar_id":"","url":"https://api.github.com/users/mjsteinbaugh","html_url":"https://github.com/mjsteinbaugh","followers_url":"https://api.github.com/users/mjsteinbaugh/followers","following_url":"https://api.github.com/users/mjsteinbaugh/following{/other_user}","gists_url":"https://api.github.com/users/mjsteinbaugh/gists{/gist_id}","starred_url":"https://api.github.com/users/mjsteinbaugh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mjsteinbaugh/subscriptions","organizations_url":"https://api.github.com/users/mjsteinbaugh/orgs","repos_url":"https://api.github.com/users/mjsteinbaugh/repos","events_url":"https://api.github.com/users/mjsteinbaugh/events{/privacy}","received_events_url":"https://api.github.com/users/mjsteinbaugh/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2017-11-02T12:12:41Z","updated_at":"2017-11-02T12:12:44Z","closed_at":null,"author_association":"OWNER","pull_request":{"url":"https://api.github.com/repos/steinbaugh/basejump/pulls/54","html_url":"https://github.com/steinbaugh/basejump/pull/54","diff_url":"https://github.com/steinbaugh/basejump/pull/54.diff","patch_url":"https://github.com/steinbaugh/basejump/pull/54.patch"},"body":"- Stopped exporting the internal functions previously used in bcbio packages.\r\n- Converted `detectHPC()`, `transmit()`, and `writeCounts()` to standard functions.\r\n- Added deprecation warning to `pct()` function.\r\n- Removed exported Rd files for internal functions.\r\n- Updated `loadData()`, `loadRemoteData()`, and `saveData()` with replace/overwrite support. Made the `loadData*` functions opinionated, rejecting R data files containing multiple objects. The file name of the object must match the internal object name.\r\n- Made `NULL` returns invisible for bcbio file utility functions.\r\n- Improved file integrity checks for `readSampleMetadataFile()`. Removed the object to subset the file using pattern checking (`pattern`, `patternCol` arguments). This method was underpowered and not that useful.\r\n- Reorganized example data URLs for bcbio files.\r\n- `saveData()` now uses bzip2 compression by default instead of gzip.\r\n- Improved code coverage in unit tests. Almost back to 100%."},"comment":{"url":"https://api.github.com/repos/steinbaugh/basejump/issues/comments/341402590","html_url":"https://github.com/steinbaugh/basejump/pull/54#issuecomment-341402590","issue_url":"https://api.github.com/repos/steinbaugh/basejump/issues/54","id":341402590,"user":{"login":"codecov[bot]","id":22429695,"avatar_url":"https://avatars2.githubusercontent.com/in/254?v=4","gravatar_id":"","url":"https://api.github.com/users/codecov%5Bbot%5D","html_url":"https://github.com/apps/codecov","followers_url":"https://api.github.com/users/codecov%5Bbot%5D/followers","following_url":"https://api.github.com/users/codecov%5Bbot%5D/following{/other_user}","gists_url":"https://api.github.com/users/codecov%5Bbot%5D/gists{/gist_id}","starred_url":"https://api.github.com/users/codecov%5Bbot%5D/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/codecov%5Bbot%5D/subscriptions","organizations_url":"https://api.github.com/users/codecov%5Bbot%5D/orgs","repos_url":"https://api.github.com/users/codecov%5Bbot%5D/repos","events_url":"https://api.github.com/users/codecov%5Bbot%5D/events{/privacy}","received_events_url":"https://api.github.com/users/codecov%5Bbot%5D/received_events","type":"Bot","site_admin":false},"created_at":"2017-11-02T12:12:44Z","updated_at":"2017-11-02T12:12:44Z","author_association":"NONE","body":"# [Codecov](https://codecov.io/gh/steinbaugh/basejump/pull/54?src=pr&el=h1) Report\n> Merging [#54](https://codecov.io/gh/steinbaugh/basejump/pull/54?src=pr&el=desc) into [master](https://codecov.io/gh/steinbaugh/basejump/commit/1b39816b53ac1a16b8656394ab532e53d8ecf8bc?src=pr&el=desc) will **increase** coverage by `5.86%`.\n> The diff coverage is `100%`.\n\n[![Impacted file tree graph](https://codecov.io/gh/steinbaugh/basejump/pull/54/graphs/tree.svg?width=650&height=150&src=pr&token=Ipa1ocaf9W)](https://codecov.io/gh/steinbaugh/basejump/pull/54?src=pr&el=tree)\n\n```diff\n@@            Coverage Diff            @@\n##           master     #54      +/-   ##\n=========================================\n+ Coverage   93.24%   99.1%   +5.86%     \n=========================================\n  Files          54      54              \n  Lines        1524    1561      +37     \n=========================================\n+ Hits         1421    1547     +126     \n+ Misses        103      14      -89\n```\n\n\n| [Impacted Files](https://codecov.io/gh/steinbaugh/basejump/pull/54?src=pr&el=tree) | Coverage Δ | |\n|---|---|---|\n| [R/methods-readFileByExtension.R](https://codecov.io/gh/steinbaugh/basejump/pull/54?src=pr&el=tree#diff-Ui9tZXRob2RzLXJlYWRGaWxlQnlFeHRlbnNpb24uUg==) | `97.72% <ø> (+1.98%)` | :arrow_up: |\n| [R/AllGenerics.R](https://codecov.io/gh/steinbaugh/basejump/pull/54?src=pr&el=tree#diff-Ui9BbGxHZW5lcmljcy5S) | `100% <ø> (ø)` | :arrow_up: |\n| [R/methods-prepareAnnotable.R](https://codecov.io/gh/steinbaugh/basejump/pull/54?src=pr&el=tree#diff-Ui9tZXRob2RzLXByZXBhcmVBbm5vdGFibGUuUg==) | `100% <ø> (+17.74%)` | :arrow_up: |\n| [R/transmit.R](https://codecov.io/gh/steinbaugh/basejump/pull/54?src=pr&el=tree#diff-Ui90cmFuc21pdC5S) | `97.87% <ø> (ø)` | |\n| [R/writeCounts.R](https://codecov.io/gh/steinbaugh/basejump/pull/54?src=pr&el=tree#diff-Ui93cml0ZUNvdW50cy5S) | `100% <ø> (ø)` | |\n| [R/methods-sampleYAML.R](https://codecov.io/gh/steinbaugh/basejump/pull/54?src=pr&el=tree#diff-Ui9tZXRob2RzLXNhbXBsZVlBTUwuUg==) | `96.96% <ø> (+6.06%)` | :arrow_up: |\n| [R/methods-sampleYAMLMetrics.R](https://codecov.io/gh/steinbaugh/basejump/pull/54?src=pr&el=tree#diff-Ui9tZXRob2RzLXNhbXBsZVlBTUxNZXRyaWNzLlI=) | `85.71% <ø> (ø)` | :arrow_up: |\n| [R/methods-prepareTemplate.R](https://codecov.io/gh/steinbaugh/basejump/pull/54?src=pr&el=tree#diff-Ui9tZXRob2RzLXByZXBhcmVUZW1wbGF0ZS5S) | `100% <ø> (ø)` | :arrow_up: |\n| [R/methods-readYAML.R](https://codecov.io/gh/steinbaugh/basejump/pull/54?src=pr&el=tree#diff-Ui9tZXRob2RzLXJlYWRZQU1MLlI=) | `100% <ø> (+6.66%)` | :arrow_up: |\n| [R/methods-sampleYAMLMetadata.R](https://codecov.io/gh/steinbaugh/basejump/pull/54?src=pr&el=tree#diff-Ui9tZXRob2RzLXNhbXBsZVlBTUxNZXRhZGF0YS5S) | `100% <ø> (ø)` | :arrow_up: |\n| ... and [27 more](https://codecov.io/gh/steinbaugh/basejump/pull/54?src=pr&el=tree-more) | |\n\n------\n\n[Continue to review full report at Codecov](https://codecov.io/gh/steinbaugh/basejump/pull/54?src=pr&el=continue).\n> **Legend** - [Click here to learn more](https://docs.codecov.io/docs/codecov-delta)\n> `Δ = absolute <relative> (impact)`, `ø = not affected`, `? = missing data`\n> Powered by [Codecov](https://codecov.io/gh/steinbaugh/basejump/pull/54?src=pr&el=footer). Last update [1b39816...e1ce267](https://codecov.io/gh/steinbaugh/basejump/pull/54?src=pr&el=lastupdated). Read the [comment docs](https://docs.codecov.io/docs/pull-request-comments).\n"}}
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