PyEvoMotion 0.1.0__py3-none-any.whl → 0.1.1__py3-none-any.whl

{pyevomotion-0.1.0.dist-info → pyevomotion-0.1.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: PyEvoMotion
-Version: 0.1.0
+Version: 0.1.1
 Summary: Evolutionary motion analysis tool
 Keywords: evolution,anomalous diffusion,bioinformatics
 Author: Lucas Goiriz
@@ -27,7 +27,7 @@ _(See [Goiriz L, et al.](http://doi.org/10.1073/pnas.2303578120))_
 ## Installation
 
 > **Note:**
-> `PyEvoMotion` uses [mafft](https://mafft.cbrc.jp/alignment/software/) to do the sequence alignment. If it’s not available in your system, on the the first run of `PyEvoMotion`, it will ask to install it locally.
+> `PyEvoMotion` uses [mafft](https://mafft.cbrc.jp/alignment/software/) to do the sequence alignment. If it's not available in your system, on the first run of `PyEvoMotion`, it will ask to install it locally.
 > 
 > If so, ensure to restart your shell session or run `source ~/.bashrc` to update the PATH environment variable, so that the `mafft` executable is available in your shell.
 >
@@ -74,8 +74,6 @@ options:
   -ep, --export_plots   Export the plots of the analysis.
   -l LENGTH_FILTER, --length_filter LENGTH_FILTER
                         Length filter for the sequences (removes sequences with length less than the specified value). Default is 0.
-  -n N_THRESHOLD, --n_threshold N_THRESHOLD
-                        Minimum number of sequences required in a time interval to compute statistics. Default is 2.
   -xj, --export_json    Export the run arguments to a json file.
   -ij IMPORT_JSON, --import_json IMPORT_JSON
                         Import the run arguments from a JSON file. If this argument is passed, the other arguments are ignored. The JSON file must contain the mandatory keys 'seqs', 'meta', and 'out'.
@@ -114,4 +112,74 @@ pytest
 > Given the size of the test data, this may take a while.
 
 
+## Docker
 
+A Docker image containing a virtual environment with `PyEvoMotion` pre-installed, its dependencies, the test data is available at `ghcr.io/luksgrin/pyevomotion:latest` and the manuscript's original figure script is available at `ghcr.io/luksgrin/pyevomotion-fig:latest`.
+
+Pull the image from by running:
+
+```bash
+docker pull ghcr.io/luksgrin/pyevomotion:latest
+```
+
+Alternatively, to build the main image, run:
+
+```bash
+docker build -t ghcr.io/luksgrin/pyevomotion:latest -f docker/Dockerfile
+```
+
+### Running the container
+
+To start an interactive container:
+
+```bash
+docker run -it ghcr.io/luksgrin/pyevomotion:latest
+```
+
+This will open a prompt that displays a welcome message and allows you to start using `PyEvoMotion` right away.
+
+### Included data
+
+The image includes (heavy) input files (FASTA and metadata) in:
+
+```bash
+/home/pyevomotion/pyevomotion-*/tests/data/test3
+```
+
+which are used by the test suite (and are automatically downloaded and extracted if not present, thereby using the containerized version is more convenient).
+
+Also, the source script for figure generation (along with the pre-generated results of running `PyEvoMotion`) is already available under:
+
+```bash
+/home/pyevomotion/pyevomotion-*/share
+```
+
+Do note that if all the contents within
+
+```bash
+/home/pyevomotion/pyevomotion-*/share
+```
+
+are deleted except for the `manuscript_figure.py` script, it is still possible to generate the figure (although it will take much longer since the dataset's stats must be computed by `PyEvoMotion`).
+
+### Running tests
+
+Once inside the container, run:
+
+```bash
+cd pyevomotion-*
+pytest
+```
+
+This will execute the test suite included with the source.
+
+### Reproducing the Figure from the original manuscript
+
+To reproduce the figure from the original manuscript, run:
+
+```bash
+cd pyevomotion-*
+python share/manuscript_figure.py export
+```
+
+The figure will be saved in the `share` directory. Font warnings may appear — they are safe to ignore and do not affect the scientific content of the figure, only the styling.

pyevomotion-0.1.1.dist-info/RECORD

@@ -0,0 +1,31 @@
+PyEvoMotion/__init__.py,sha256=NqFDD-EZBzouzTwXozZqhPC9sLr7GQaElRKtP0tkHoE,568
+PyEvoMotion/cli.py,sha256=U_zX6Y9kU9l-vtC9BeR1ebT7PLogAqpBNHs-DT552vI,15322
+PyEvoMotion/core/__init__.py,sha256=1I-NkFFh6ljLgB_mqQVFLNvCrVKEHLVxa_5dsv3ihWQ,450
+PyEvoMotion/core/base.py,sha256=0NQ0njPIFn9sL4PdymWE3LYcOmrl3LyCsMDRtAPCRVM,16851
+PyEvoMotion/core/core.py,sha256=ynsHkqZMZZaoikRp1967smHaSzYVX658LjVewZtdQnI,19927
+PyEvoMotion/core/parser.py,sha256=w23KzX0jl3NLS0WYjAY1s_2VFEqfn6EoTrQXmGRRXfg,17323
+PyEvoMotion/utils.py,sha256=Ye3eL1RXZOZzzs2KZy0R45u06DOtLYo-zqE45tN2t7g,2859
+share/anomalous_diffusion.pdf,sha256=yBjHK1dzyx1akaOjmQ8ogWhH1QUWXqCTdUHlXMhtwug,19384
+share/figUK.tsv,sha256=DnPkVfbMGfsOq9x8IAkbPzIWsmQBB1hOXChSNkNlHGo,6711825
+share/figUK_plots.pdf,sha256=-YfMSLcpsHWq4D9hwFc45LrBdL6BNEyNVNs2j_Y36M8,22865
+share/figUK_regression_results.json,sha256=GFD3av78AhVzwuJkOYpqo5NwbUSdWoxe7_2fz7Xeysk,470
+share/figUK_run_args.json,sha256=lWbeubYYU--BhEzkFHGOSF4cJ_wMhmYHwyj8Iaxqpj0,314
+share/figUK_stats.tsv,sha256=ZvzPtCtnvnXQOU9blDx-_iU3h5IUXOU94D9xCfobXWE,2055
+share/figUSA.tsv,sha256=hSPmKjCFk0a5B0XN75JhQOuhZgfcz9ZCxNrfqMrYcF0,6577552
+share/figUSA_plots.pdf,sha256=679_rgan3Eb6KsclNu5xEeIvQEGJDIN4wMzMeqq2ZvI,22271
+share/figUSA_regression_results.json,sha256=Q9t5KE_vV_-wuhRcXhnMrEMDc6BT1LFmlDu17RpigkY,468
+share/figUSA_run_args.json,sha256=-jsoE6BXQTy7-UsgoVjuCZsShgtseQ3YUxX8vIGJMN4,317
+share/figUSA_stats.tsv,sha256=BnpZs8oWgeRHiKCW8r7KrYc9YaO3i5X447jKPhtUZeQ,1751
+share/figdataUK.tsv,sha256=HMF07FNT7d3Tb2OMHuFYkRzc6vb5EQ6vj2nJBpXlXJ8,939837
+share/figdataUSA.tsv,sha256=z5yaIwcyfLo7Wr5ioE-x6_qXg9IhT_CmAJxcLTfP4jA,827811
+share/figure.pdf,sha256=9D2gy7fr-LC52kRfD09aZP8Z8jmY_7K8IhigzIgAK5U,24194
+share/generate_sequences_from_synthdata.py,sha256=_2IdMgcOB7SxAq30iypA-VypSmZyZmMhA8otKQnkfAw,3443
+share/mafft_install.sh,sha256=pCw70UsKkkNXUsZMwQlQ2b4zSXFrBA7jAj9iOfGLzUw,1007
+share/manuscript_figure.py,sha256=G61puV4VjfTgXbokD380aSB0C4Wo9HEJ8y3kw0_Z-TQ,24474
+share/synth_figure.pdf,sha256=2hckyY0Uie16yn3YH5B1LE2lakOJGLzSbF6GHelvSEE,26350
+share/uk_time_windows.pdf,sha256=U1zAMRgZxvfpfMr2ahUqHGYSxPVoDRQTGJSF96NJFck,35022
+share/weekly_size.pdf,sha256=9hn6U8IBWQvZTR8hNLo3r3Kb4hwB7awxlt31_clcHjA,14602
+pyevomotion-0.1.1.dist-info/METADATA,sha256=jgRSgfXK41_APjXUKNA41jggW_bGx9zYxnULz1B1ulQ,7833
+pyevomotion-0.1.1.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
+pyevomotion-0.1.1.dist-info/entry_points.txt,sha256=UMzoojYwQi-713hRggkQXUIfGNygUARhTdGs77Usp7s,53
+pyevomotion-0.1.1.dist-info/RECORD,,