abutils - pypi Package Compare versions

Comparing version 0.5.1 to 0.5.2

abutils.egg-info/PKG-INFO

 Metadata-Version: 2.4
 Name: abutils
-Version: 0.5.1
+Version: 0.5.2
 Summary: Utilities for analysis of adaptive immune receptor repertoire (AIRR) data
@@ -21,3 +21,3 @@ Home-page: https://github.com/briney/abutils
 License-File: LICENSE
-Requires-Dist: abstar>=0.6.3
+Requires-Dist: abstar>=0.7
 Requires-Dist: baltic
@@ -30,3 +30,3 @@ Requires-Dist: biopython>=1.78
 Requires-Dist: natsort
-Requires-Dist: numpy
+Requires-Dist: numpy<2
 Requires-Dist: pandas
@@ -74,9 +74,11 @@ Requires-Dist: paramiko
   - Download: [pypi.python.org/pypi/abutils](https://pypi.python.org/pypi/abutils)  
-  <!-- - Docker: [hub.docker.com/r/briney/abstar/](https://hub.docker.com/r/briney/abstar/)   -->  
+  - Docker: [hub.docker.com/r/brineylab/datascience/](https://hub.docker.com/r/brineylab/datascience/)  
   
-### install  
-`pip install abutils`  
+## install  
+``` bash
+pip install abutils
+```
 
 
-### api  
+## api  
 We've tried to design the  `abutils` API to be intuitive yet powerful, with the goal of enabling both interactive analyses (via environments like Jupyter notebooks) as well as integration of `abutils` tools into more complex analysis pipelines and/or standalone software tools. See the [documentation](http://abutils.readthedocs.org) for more detail about the API. As always, any feedback is greatly appreciated!!  
@@ -87,10 +89,10 @@
 You can run the complete `abutils` test suite by first installing `pytest`:
-```
+``` bash
 pip install pytest
 ```
 
-followed by:
+and then running:
 
-```
-git clone https://github.com/briney/abutils
+``` bash
+git clone https://github.com/brineylab/abutils
 cd abutils
@@ -100,3 +102,3 @@ pytest
 
-This test suite is automatically run following every commit, and is tested against all supported versions of Python.
+This test suite is automatically run against all supported versions of Python following every commit.
   
@@ -110,4 +112,3 @@
 biopython  
-celery  
-ete3  
+dnachisel  
 fastcluster  
@@ -119,8 +120,12 @@ matplotlib
 pandas  
-paramiko  
 parasail  
+polars  
+prettytable  
+pyarrow  
+pyfamsa  
+pyfastx  
 pytest  
 python-circos  
-python-Levenshtein  
 pyyaml  
+rapidfuzz  
 sample-sheet  
@@ -131,17 +136,13 @@ scikit-learn
 smart_open  
+tqdm  
   
-All of the above dependencies can be installed with `pip`, and will be installed automatically when installing `abutils` with `pip`.  
-  
-`abutils` packages several additional external binaries that are required for specific functions:
+`abutils` includes several additional binaries that are required for certain functionality:
 
 * ``abutils.tl.mafft`` uses [MAFFT](https://mafft.cbrc.jp/alignment/software/)
 * ``abutils.tl.muscle`` uses [MUSCLE](https://www.drive5.com/muscle/)
-* ``abutils.tl.cluster`` requires:
-  * [CD-HIT](https://cd-hit.org)
-  * [MMseqs2](https://github.com/soedinglab/MMseqs2)
-  * [VSEARCH](https://github.com/torognes/vsearch)
-* ``abutils.tl.fasttree`` requires [FastTree](http://www.microbesonline.org/fasttree/)
+* ``abutils.tl.cluster`` uses [CD-HIT](https://cd-hit.org), [MMseqs2](https://github.com/soedinglab/MMseqs2), and [VSEARCH](https://github.com/torognes/vsearch)
+* ``abutils.tl.fasttree`` uses [FastTree](http://www.microbesonline.org/fasttree/)
 
-Althogh these binaries are all packaged into `abutils`, each respective `abutils` function provides the option to supply a different binary path in case you'd prefer to use a different version or an alternate compilation.  
+Although these binaries are all packaged into `abutils`, each respective `abutils.tl` function provides the option to supply a alternate binary path in case you'd prefer to use a different version.  
 
 

abutils.egg-info/requires.txt

@@ -1,2 +0,2 @@
-abstar>=0.6.3
+abstar>=0.7
 baltic
@@ -9,3 +9,3 @@ biopython>=1.78
 natsort
-numpy
+numpy<2
 pandas
@@ -12,0 +12,0 @@ paramiko

abutils/version.py

@@ -6,2 +6,2 @@ # Store the version here so:
 
-__version__ = "0.5.1"
+__version__ = "0.5.2"

PKG-INFO

 Metadata-Version: 2.4
 Name: abutils
-Version: 0.5.1
+Version: 0.5.2
 Summary: Utilities for analysis of adaptive immune receptor repertoire (AIRR) data
@@ -21,3 +21,3 @@ Home-page: https://github.com/briney/abutils
 License-File: LICENSE
-Requires-Dist: abstar>=0.6.3
+Requires-Dist: abstar>=0.7
 Requires-Dist: baltic
@@ -30,3 +30,3 @@ Requires-Dist: biopython>=1.78
 Requires-Dist: natsort
-Requires-Dist: numpy
+Requires-Dist: numpy<2
 Requires-Dist: pandas
@@ -74,9 +74,11 @@ Requires-Dist: paramiko
   - Download: [pypi.python.org/pypi/abutils](https://pypi.python.org/pypi/abutils)  
-  <!-- - Docker: [hub.docker.com/r/briney/abstar/](https://hub.docker.com/r/briney/abstar/)   -->  
+  - Docker: [hub.docker.com/r/brineylab/datascience/](https://hub.docker.com/r/brineylab/datascience/)  
   
-### install  
-`pip install abutils`  
+## install  
+``` bash
+pip install abutils
+```
 
 
-### api  
+## api  
 We've tried to design the  `abutils` API to be intuitive yet powerful, with the goal of enabling both interactive analyses (via environments like Jupyter notebooks) as well as integration of `abutils` tools into more complex analysis pipelines and/or standalone software tools. See the [documentation](http://abutils.readthedocs.org) for more detail about the API. As always, any feedback is greatly appreciated!!  
@@ -87,10 +89,10 @@
 You can run the complete `abutils` test suite by first installing `pytest`:
-```
+``` bash
 pip install pytest
 ```
 
-followed by:
+and then running:
 
-```
-git clone https://github.com/briney/abutils
+``` bash
+git clone https://github.com/brineylab/abutils
 cd abutils
@@ -100,3 +102,3 @@ pytest
 
-This test suite is automatically run following every commit, and is tested against all supported versions of Python.
+This test suite is automatically run against all supported versions of Python following every commit.
   
@@ -110,4 +112,3 @@
 biopython  
-celery  
-ete3  
+dnachisel  
 fastcluster  
@@ -119,8 +120,12 @@ matplotlib
 pandas  
-paramiko  
 parasail  
+polars  
+prettytable  
+pyarrow  
+pyfamsa  
+pyfastx  
 pytest  
 python-circos  
-python-Levenshtein  
 pyyaml  
+rapidfuzz  
 sample-sheet  
@@ -131,17 +136,13 @@ scikit-learn
 smart_open  
+tqdm  
   
-All of the above dependencies can be installed with `pip`, and will be installed automatically when installing `abutils` with `pip`.  
-  
-`abutils` packages several additional external binaries that are required for specific functions:
+`abutils` includes several additional binaries that are required for certain functionality:
 
 * ``abutils.tl.mafft`` uses [MAFFT](https://mafft.cbrc.jp/alignment/software/)
 * ``abutils.tl.muscle`` uses [MUSCLE](https://www.drive5.com/muscle/)
-* ``abutils.tl.cluster`` requires:
-  * [CD-HIT](https://cd-hit.org)
-  * [MMseqs2](https://github.com/soedinglab/MMseqs2)
-  * [VSEARCH](https://github.com/torognes/vsearch)
-* ``abutils.tl.fasttree`` requires [FastTree](http://www.microbesonline.org/fasttree/)
+* ``abutils.tl.cluster`` uses [CD-HIT](https://cd-hit.org), [MMseqs2](https://github.com/soedinglab/MMseqs2), and [VSEARCH](https://github.com/torognes/vsearch)
+* ``abutils.tl.fasttree`` uses [FastTree](http://www.microbesonline.org/fasttree/)
 
-Althogh these binaries are all packaged into `abutils`, each respective `abutils` function provides the option to supply a different binary path in case you'd prefer to use a different version or an alternate compilation.  
+Although these binaries are all packaged into `abutils`, each respective `abutils.tl` function provides the option to supply a alternate binary path in case you'd prefer to use a different version.  
 
 

README.md

@@ -14,9 +14,11 @@ ![](https://img.shields.io/pypi/v/abutils.svg?colorB=blue)
   - Download: [pypi.python.org/pypi/abutils](https://pypi.python.org/pypi/abutils)  
-  <!-- - Docker: [hub.docker.com/r/briney/abstar/](https://hub.docker.com/r/briney/abstar/)   -->  
+  - Docker: [hub.docker.com/r/brineylab/datascience/](https://hub.docker.com/r/brineylab/datascience/)  
   
-### install  
-`pip install abutils`  
+## install  
+``` bash
+pip install abutils
+```
 
 
-### api  
+## api  
 We've tried to design the  `abutils` API to be intuitive yet powerful, with the goal of enabling both interactive analyses (via environments like Jupyter notebooks) as well as integration of `abutils` tools into more complex analysis pipelines and/or standalone software tools. See the [documentation](http://abutils.readthedocs.org) for more detail about the API. As always, any feedback is greatly appreciated!!  
@@ -27,10 +29,10 @@
 You can run the complete `abutils` test suite by first installing `pytest`:
-```
+``` bash
 pip install pytest
 ```
 
-followed by:
+and then running:
 
-```
-git clone https://github.com/briney/abutils
+``` bash
+git clone https://github.com/brineylab/abutils
 cd abutils
@@ -40,3 +42,3 @@ pytest
 
-This test suite is automatically run following every commit, and is tested against all supported versions of Python.
+This test suite is automatically run against all supported versions of Python following every commit.
   
@@ -50,4 +52,3 @@
 biopython  
-celery  
-ete3  
+dnachisel  
 fastcluster  
@@ -59,8 +60,12 @@ matplotlib
 pandas  
-paramiko  
 parasail  
+polars  
+prettytable  
+pyarrow  
+pyfamsa  
+pyfastx  
 pytest  
 python-circos  
-python-Levenshtein  
 pyyaml  
+rapidfuzz  
 sample-sheet  
@@ -71,17 +76,13 @@ scikit-learn
 smart_open  
+tqdm  
   
-All of the above dependencies can be installed with `pip`, and will be installed automatically when installing `abutils` with `pip`.  
-  
-`abutils` packages several additional external binaries that are required for specific functions:
+`abutils` includes several additional binaries that are required for certain functionality:
 
 * ``abutils.tl.mafft`` uses [MAFFT](https://mafft.cbrc.jp/alignment/software/)
 * ``abutils.tl.muscle`` uses [MUSCLE](https://www.drive5.com/muscle/)
-* ``abutils.tl.cluster`` requires:
-  * [CD-HIT](https://cd-hit.org)
-  * [MMseqs2](https://github.com/soedinglab/MMseqs2)
-  * [VSEARCH](https://github.com/torognes/vsearch)
-* ``abutils.tl.fasttree`` requires [FastTree](http://www.microbesonline.org/fasttree/)
+* ``abutils.tl.cluster`` uses [CD-HIT](https://cd-hit.org), [MMseqs2](https://github.com/soedinglab/MMseqs2), and [VSEARCH](https://github.com/torognes/vsearch)
+* ``abutils.tl.fasttree`` uses [FastTree](http://www.microbesonline.org/fasttree/)
 
-Althogh these binaries are all packaged into `abutils`, each respective `abutils` function provides the option to supply a different binary path in case you'd prefer to use a different version or an alternate compilation.  
+Although these binaries are all packaged into `abutils`, each respective `abutils.tl` function provides the option to supply a alternate binary path in case you'd prefer to use a different version.  
 
 

requirements.txt

@@ -1,4 +0,4 @@
-abstar>=0.6.3
+abstar>=0.7
 baltic
-biopython >= 1.78
+biopython>=1.78
 # celery
@@ -11,3 +11,3 @@ dnachisel
 natsort
-numpy
+numpy<2
 pandas
@@ -14,0 +14,0 @@ paramiko

Alert delta unavailable

Currently unable to show alert delta for PyPI packages.

Worsened metrics

Total package byte prevSize

228935669

0