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physcraper

Welcome to Physcraper’s repository! Automatic gene tree updating using the Open Tree of Life.

https://github.com/mctavishlab/physcraper

Science Score: 20.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov
  • ✓
    Committers with academic emails
    1 of 7 committers (14.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.1%) to scientific vocabulary

Keywords

bioinformatics biology python
Last synced: 6 months ago · JSON representation

Repository

Welcome to Physcraper’s repository! Automatic gene tree updating using the Open Tree of Life.

Basic Info
Statistics
  • Stars: 13
  • Watchers: 6
  • Forks: 6
  • Open Issues: 36
  • Releases: 0
Topics
bioinformatics biology python
Created over 10 years ago · Last pushed almost 4 years ago
Metadata Files
Readme License

README.Rmd 

---
output: github_document
---



```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  results = "asis",
  echo = TRUE,
  comment = "#>"
)
IS_README <- TRUE
```

```{r child="docs/mds/intro-logo.md"}

```

# Welcome to Physcraper’s repository!

```{r child="docs/mds/intro-badges.md"}

```








```{r child="docs/mds/intro-part1.md"}

```

Physcraper also leverages on programmatic tools from the [TreeBASE](https://treebase.org/treebase-web/urlAPI.html) project and [NCBI](https://www.ncbi.nlm.nih.gov/home/develop/api/), as well as multiple software projects listed as [requirements](#requirements) below, to create an automatic and reproducible workflow for phylogenetics.

You are now on the code repository. Please refer to Physcraper’s
[documentation website](https://physcraper.readthedocs.io/en/main/)
for more details on:

- [installation](https://physcraper.readthedocs.io/en/main/install.html)
instructions using an Anaconda or a Virtualenv Python virtual
environment,
- [function](https://physcraper.readthedocs.io/en/main/apidocs.html)
usage,
- finding and choosing a [starting dataset](https://physcraper.readthedocs.io/en/main/find-trees.html),
- [running](https://physcraper.readthedocs.io/en/main/run.html) a full analysis,
- [visualizing and analysing](https://physcraper.readthedocs.io/en/main/results.html) results,
- real life [examples](https://physcraper.readthedocs.io/en/main/examples.html), and
- instructions for [developers](https://physcraper.readthedocs.io/en/main/CONTRIBUTING.html), and specifically on how to [update this readme](https://physcraper.readthedocs.io/en/main/CONTRIBUTING.html#updating-the-readme).


:hamster: :palm_tree: :frog: :ear_of_rice: :panda_face: :tulip: :octopus: :blossom: :whale: :mushroom: :ant: :cactus: :fish: :maple_leaf: :water_buffalo: 🦠 :shell: :bug: :octocat:


```{r child="docs/mds/citation.md"}

```


```{r child="docs/mds/license.md"}

```


```{r child="docs/mds/contact.md"}

```


```{r child="docs/mds/updating-the-readme.md"}

```

Owner

  • Name: McTavishLab
  • Login: McTavishLab
  • Kind: organization

GitHub Events

Total
Last Year

Committers

Last synced: 6 months ago

All Time
  • Total Commits: 2,011
  • Total Committers: 7
  • Avg Commits per committer: 287.286
  • Development Distribution Score (DDS): 0.563
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Martha Kandziora m****a@y****m 879
Emily Jane McTavish e****h@g****m 805
Luna Sare s****a@g****m 298
Matthias Bussonnier m****r@u****u 22
Matthias Bussonnier b****s@g****m 5
Mark T. Holder m****r@g****m 1
Your Name y****u@e****m 1
Committer Domains (Top 20 + Academic)
ucmerced.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 73
  • Total pull requests: 27
  • Average time to close issues: 7 months
  • Average time to close pull requests: 7 days
  • Total issue authors: 7
  • Total pull request authors: 2
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.22
  • Merged pull requests: 26
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • LunaSare (32)
  • snacktavish (31)
  • mkandziora (5)
  • shchurch (2)
  • jtfield (1)
  • Carreau (1)
  • lskatz (1)
Pull Request Authors
  • snacktavish (24)
  • LunaSare (3)
Top Labels
Issue Labels
pyopensci-review (16) enhancement (3) done (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 25 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 7
  • Total maintainers: 1
pypi.org: physcraper

Physcraper

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 25 Last month
Rankings
Dependent packages count: 10.1%
Forks count: 13.3%
Stargazers count: 16.1%
Average: 18.4%
Dependent repos count: 21.6%
Downloads: 31.0%
Maintainers (1)
snacktavish
Last synced: 6 months ago

Dependencies

requirements.txt pypi
  • DateTime *
  • DendroPy *
  • argparse *
  • biopython ==1.76
  • configparser *
  • coverage *
  • docutils <0.18
  • future *
  • m2r2 *
  • nexson *
  • numpy *
  • pandas *
  • pytest *
  • pytest-cov *
  • pytest-xdist *
  • recommonmark *
  • requests *
  • sh *
  • sphinx *
  • urllib3 >=1.23
setup.py pypi
  • DateTime *
  • DendroPy *
  • argparse *
  • biopython ==1.76
  • configparser *
  • nexson *
  • numpy *
  • opentree *
  • pandas *
  • requests *
  • sh *
  • urllib3 >=1.23
  • wget *