Name change to kameris

.travis.yml

@@ -26,7 +26,7 @@ jobs:
       language: generic
       if: branch = master AND type != pull_request
       install:
-        - brew upgrade python
+        - brew update && brew uninstall --ignore-dependencies --force python && brew install https://raw.githubusercontent.com/Homebrew/homebrew-core/f2a764ef944b1080be64bd88dca9a1d80130c558/Formula/python.rb
         - unlink /usr/local/bin/python; ln -s /usr/local/bin/python3 /usr/local/bin/python
         - export PATH=/usr/local/bin:$PATH
         - sudo mkdir -p /usr/local/man

Makefile

@@ -1,7 +1,6 @@
 .PHONY: all pip-package bin-package distribute distribute-pip distribute-bin test lint install uninstall clean
 
-CLEAN_CMD = bash -c 'rm -rf build dist modmap_toolkit.egg-info && find . -type f \( -name '*.pyc' -o -name '*.pyo' \) -delete'
-VERSION_NUMBER = $(shell python -c 'import modmap_toolkit; print(modmap_toolkit.__version__)')
+VERSION_NUMBER = $(shell python -c 'import kameris; print(kameris.__version__)')
 ifeq ($(OS),Windows_NT)
 	EXE_SUFFIX = -windows.exe
 else
@@ -23,7 +22,7 @@ pip-package: clean
 
 bin-package:
 	python -m pip install --upgrade pyinstaller
-	python -m PyInstaller modmap-toolkit.spec
+	python -m PyInstaller kameris.spec
 
 distribute: distribute-pip distribute-bin
 
@@ -32,24 +31,24 @@ distribute-pip: pip-package
 	python -m twine upload dist/*.whl
 
 distribute-bin: bin-package
-	tools/github-release/github-release$(EXE_SUFFIX) upload --user stephensolis --repo modmap-toolkit \
+	tools/github-release/github-release$(EXE_SUFFIX) upload --user stephensolis --repo kameris \
 															--tag v$(VERSION_NUMBER) \
-															--name modmap-toolkit$(EXE_SUFFIX) \
-															--file dist/modmap-toolkit$(EXE_SUFFIX)
+															--name kameris$(EXE_SUFFIX) \
+															--file dist/kameris$(EXE_SUFFIX)
 
 
 test: lint
 
 lint:
-	python -m flake8 modmap_toolkit modmap-toolkit.py setup.py
+	python -m flake8 kameris kameris.py setup.py
 
 
 install:
 	python -m pip install -e .
 
 uninstall:
-	python -m pip uninstall modmap-toolkit
+	python -m pip uninstall kameris
 
 
 clean:
-	$(CLEAN_CMD)
+	bash -c 'rm -rf build dist kameris.egg-info && find . -type f \( -name '*.pyc' -o -name '*.pyo' \) -delete'

README.md

@@ -1,42 +1,42 @@
 <h1 align="center">
     <br>
-    <img src="https://raw.githubusercontent.com/stephensolis/modmap-toolkit/master/logo/logo.png" alt="modmap-toolkit" width="200">
+    <img src="https://raw.githubusercontent.com/stephensolis/kameris/master/logo/logo.png" alt="kameris" width="200">
     <br>
-    modmap-toolkit
+    Kameris
     <br>
 </h1>
 
 <h4 align="center">A fast, user-friendly analysis and evaluation pipeline for some DNA sequence classification tasks.</h4>
 
 <p align="center">
-    <a href="https://pypi.python.org/pypi/modmap-toolkit">
-        <img src="https://badge.fury.io/py/modmap-toolkit.svg" alt="PyPI">
+    <a href="https://pypi.python.org/pypi/kameris">
+        <img src="https://badge.fury.io/py/kameris.svg" alt="PyPI">
     </a>
     <img src="http://img.shields.io/:license-mit-blue.svg" alt="License">
     &nbsp;
-    <a href="https://travis-ci.org/stephensolis/modmap-toolkit">
-        <img src="https://travis-ci.org/stephensolis/modmap-toolkit.svg?branch=master" alt="Travis">
+    <a href="https://travis-ci.org/stephensolis/kameris">
+        <img src="https://travis-ci.org/stephensolis/kameris.svg?branch=master" alt="Travis">
     </a>
-    <a href="https://ci.appveyor.com/project/stephensolis/modmap-toolkit">
+    <a href="https://ci.appveyor.com/project/stephensolis/kameris">
         <img src="https://ci.appveyor.com/api/projects/status/v22hru9wvvdhsv8q?svg=true" alt="Appveyor">
     </a>
     &nbsp;
-    <a href="https://www.codacy.com/app/stephensolis/modmap-toolkit">
+    <a href="https://www.codacy.com/app/stephensolis/kameris">
         <img src="https://api.codacy.com/project/badge/Grade/2286db6fde1d4b729127f820d7896cd0" alt="Codacy">
     </a>
-    <a href="https://codebeat.co/projects/github-com-stephensolis-modmap-toolkit-maste">
-        <img src="https://codebeat.co/badges/d344663e-21af-402e-a95f-b030b6a6ca2d" alt="Codebeat">
+    <a href="https://codebeat.co/projects/github-com-stephensolis-kameris-master">
+        <img src="https://codebeat.co/badges/5826ce1f-ba26-4cd4-a641-d33845023d79" alt="Codebeat">
     </a>
-    <a href="https://codeclimate.com/github/stephensolis/modmap-toolkit/maintainability">
-        <img src="https://api.codeclimate.com/v1/badges/7dcf996e9fcb35d8db7d/maintainability" alt="Codeclimate">
+    <a href="https://codeclimate.com/github/stephensolis/kameris/maintainability">
+        <img src="https://api.codeclimate.com/v1/badges/0ea51d670aba5f65c707/maintainability" alt="Codeclimate">
     </a>
 </p>
 
 This project uses:
 
-- [stephensolis/modmap-generator-cpp](https://github.com/stephensolis/modmap-generator-cpp) to generate kmer count vectors and distance matrices
+- [stephensolis/kameris-backend](https://github.com/stephensolis/kameris-backend) to generate k-mer count vectors and distance matrices
 - [scikit-learn](http://scikit-learn.org/) for supervised classifiers
-- [Wolfram Mathematica](https://www.wolfram.com/mathematica/) and code based on [stephensolis/modmap-generator-mma](https://github.com/stephensolis/modmap-generator-mma) to generate interactive plots
+- [Wolfram Mathematica](https://www.wolfram.com/mathematica/) and code based on [stephensolis/modmap-generator](https://github.com/stephensolis/modmap-generator) to generate interactive plots
 - [NumPy](http://www.numpy.org/) and [SciPy](https://www.scipy.org/) for MultiDimensional Scaling (MDS)
 
 ## License ![License](http://img.shields.io/:license-mit-blue.svg)

modmap-toolkit.py → kameris.py

@@ -5,5 +5,5 @@
 import multiprocessing
 multiprocessing.freeze_support()
 
-from modmap_toolkit.__main__ import main  # NOQA
+from kameris.__main__ import main  # NOQA
 main()

modmap-toolkit.spec → kameris.spec

@@ -1,18 +1,18 @@
-from modmap_toolkit.utils.platform_utils import platform_name
+from kameris.utils.platform_utils import platform_name
 
 
-a = Analysis(['modmap-toolkit.py'],
+a = Analysis(['kameris.py'],
              pathex=[os.getcwd()],
              binaries=[],
              datas=[
-                ('modmap_toolkit/scripts/make_plots.wls', 'modmap_toolkit/scripts'),
-                ('modmap_toolkit/scripts/generation_cgr_' + platform_name() + '_*', 'modmap_toolkit/scripts'),
-                ('modmap_toolkit/scripts/generation_dists_' + platform_name() + '_*', 'modmap_toolkit/scripts')
+                ('kameris/scripts/make_plots.wls', 'kameris/scripts'),
+                ('kameris/scripts/generation_cgr_' + platform_name() + '_*', 'kameris/scripts'),
+                ('kameris/scripts/generation_dists_' + platform_name() + '_*', 'kameris/scripts')
              ],
              hiddenimports=[
                  'sklearn.neighbors.typedefs', 'sklearn.neighbors.quad_tree', 'sklearn.tree._utils',
                  'scipy._lib.messagestream',
-                 'modmap_toolkit.subcommands.run_job', 'modmap_toolkit.subcommands.summarize'
+                 'kameris.subcommands.run_job', 'kameris.subcommands.summarize'
              ],
              hookspath=[],
              runtime_hooks=[],
@@ -25,7 +25,7 @@ exe = EXE(pyz,
           a.binaries,
           a.zipfiles,
           a.datas,
-          name='modmap-toolkit-' + platform_name(),
+          name='kameris-' + platform_name(),
           debug=False,
           strip=False,
           upx=False,

modmap_toolkit/__init__.py → kameris/__init__.py

@@ -1,3 +1,3 @@
 from __future__ import unicode_literals
 
-__version__ = '0.3.dev12'
+__version__ = '0.4.dev5'

modmap_toolkit/__main__.py → kameris/__main__.py

@@ -28,7 +28,7 @@ def main():
 
     args = parser.parse_args()
     run_module = importlib.import_module('.subcommands.' + args.module_name,
-                                         'modmap_toolkit')
+                                         'kameris')
     run_module.run(args)
 
 

modmap_toolkit/job_steps/__init__.py → kameris/job_steps/__init__.py

@@ -1,17 +1,17 @@
 from __future__ import absolute_import, division, unicode_literals
 
+from . import backend
 from . import classify
 from . import command
 from . import mds
-from . import mmg
 from . import selection
 
 
 step_runners = {
     'classify': classify.run_classify_step,
     'command': command.run_command_step,
-    'kmers': mmg.run_mmg_kmers,
-    'distances': mmg.run_mmg_dists,
+    'kmers': backend.run_backend_kmers,
+    'distances': backend.run_backend_dists,
     'mds': mds.run_mds_step,
     'select': selection.run_select_step
 }

modmap_toolkit/job_steps/mmg.py → kameris/job_steps/backend.py

@@ -29,7 +29,7 @@ def binary_path(bin_name):
     ))
 
 
-def run_mmg_kmers(options, exp_options):
+def run_backend_kmers(options, exp_options):
     command.run_command_step({
         'command': '"{}" cgr "{}" "{}" {} {}'.format(
                         binary_path('generation_cgr'),
@@ -38,7 +38,7 @@ def run_mmg_kmers(options, exp_options):
     }, {})
 
 
-def run_mmg_dists(options, exp_options):
+def run_backend_dists(options, exp_options):
     command.run_command_step({
         'command': '"{}" "{}" "{}" {}'.format(
                         binary_path('generation_dists'),

modmap_toolkit/job_steps/classify.py → kameris/job_steps/classify.py

@@ -7,7 +7,7 @@
 from collections import defaultdict
 import json
 import logging
-import mmg_formats
+import kameris_formats
 import numpy as np
 import scipy.sparse as sparse
 from six import iteritems
@@ -172,20 +172,20 @@ def default(self, obj):
 
 
 def run_classify_step(options, exp_options):
-    log = logging.getLogger('modmap.classify')
+    log = logging.getLogger('kameris.classify')
 
     if options['classifiers'] == 'all':
         classifier_names = classifiers_by_name.keys()
     else:
         classifier_names = options['classifiers']
 
-    if options['features_type'] == 'mmg-dists':
-        features = mmg_formats.dist_reader \
-                              .read_matrix(options['features_file'])
+    if options['features_type'] == 'mm-dists':
+        features = kameris_formats.dist_reader \
+                                  .read_matrix(options['features_file'])
         features_mode = 'dists'
-    elif options['features_type'] == 'mmg-repr':
+    elif options['features_type'] == 'mm-repr':
         features = []
-        reader = mmg_formats.repr_reader(options['features_file'])
+        reader = kameris_formats.repr_reader(options['features_file'])
         for i in range(reader.count):
             features.append(reader.read_matrix(i, flatten=True))
 

modmap_toolkit/job_steps/command.py → kameris/job_steps/command.py

@@ -5,7 +5,7 @@
 
 
 def run_command_logged(command, **kwargs):
-    log = logging.getLogger('modmap')
+    log = logging.getLogger('kameris')
     log.info('running command "%s"', command)
     process = subprocess.Popen(command, stdout=subprocess.PIPE,
                                stderr=subprocess.STDOUT,

modmap_toolkit/job_steps/mds.py → kameris/job_steps/mds.py

@@ -2,7 +2,7 @@
 
 import json
 import logging
-import mmg_formats
+import kameris_formats
 import numpy as np
 import scipy.sparse.linalg as linalg
 
@@ -26,7 +26,7 @@ def mds(delta, dim):
 
     (eigenvals, eigenvecs) = linalg.eigsh(bMatr, k=dim)
     if (eigenvals < 0).any():
-        logging.getLogger('modmap.mds') \
+        logging.getLogger('kameris.mds') \
                .warning('some eigenvalues were negative')
 
     # not sure why eigensystem is sorted in reverse order for eigsh...
@@ -36,7 +36,7 @@ def mds(delta, dim):
 
 
 def run_mds_step(options, exp_options):
-    dists = mmg_formats.dist_reader.read_matrix(options['dists_file'])
+    dists = kameris_formats.dist_reader.read_matrix(options['dists_file'])
     points = mds(dists, options['dimensions']).tolist()
 
     with open(options['output_file'], 'w') as outfile:

modmap_toolkit/job_steps/selection.py → kameris/job_steps/selection.py

@@ -61,7 +61,7 @@ def run_select_step(options, exp_options):
         file_counter = 1
 
         for metadata_entry in tqdm(pick_group_metadata, mininterval=1,
-                                   file=job_utils.LoggerFileAdapter('modmap')):
+                                   file=job_utils.LoggerAsFile('kameris')):
             group_options = groups[metadata_entry['group']]
 
             # open archive file

modmap_toolkit/scripts/make_plots.wls → kameris/scripts/make_plots.wls

@@ -3,7 +3,7 @@
 (* plot settings *)
 
 colorScheme = {
-	Blue, Red, Green, Magenta, Yellow, Orange, Darker@Green, Cyan, Brown
+	Blue, Red, Green, Magenta, Orange, Darker@Green, Cyan, Brown, Purple, Yellow
 };
 
 

modmap_toolkit/subcommands/run_job.py → kameris/subcommands/run_job.py

@@ -164,7 +164,7 @@ def run_experiment_copy(copy_options, paths, local_dirs, job_name):
 
 
 def run_experiment_steps(steps, exp_options):
-    log = logging.getLogger('modmap')
+    log = logging.getLogger('kameris')
 
     for i, step_options in enumerate(steps):
         step_desc = "step '{}' ({}/{})".format(step_options['type'], i+1,
@@ -181,7 +181,7 @@ def run_experiment_steps(steps, exp_options):
 
 
 def setup_logging(job_name, settings):
-    log = logging.getLogger('modmap')
+    log = logging.getLogger('kameris')
     log.setLevel(logging.INFO)
     formatter = logging.Formatter('%(levelname)-8s %(message)s')
 

modmap_toolkit/subcommands/summarize.py → kameris/subcommands/summarize.py

@@ -199,9 +199,9 @@ def accuracy_for_classifier(classifier_results):
 
         if args.plot_output_dir is not None:
             num_classes = len(curr_stats['classes'])
-            if num_classes > 9:
+            if num_classes > 10:
                 print('Warning: skipping plot generation because there are '
-                      'too many classes ({} > 9)'.format(num_classes))
+                      'too many classes ({} > 10)'.format(num_classes))
             else:
                 base_output_path = os.path.join(
                     args.plot_output_dir, os.path.basename(args.job_dir)

modmap_toolkit/utils/job_utils.py → kameris/utils/job_utils.py

@@ -21,7 +21,7 @@ def call_string_extended_lambda(func_str, *args, **kwargs):  # NOQA (cache line
 
 # for formatted log output
 
-class LoggerFileAdapter:
+class LoggerAsFile:
     def __init__(self, logger_name):
         self.log = logging.getLogger(logger_name)
 
@@ -36,7 +36,7 @@ def flush(self):
 
 @contextlib.contextmanager
 def log_step(step_text, start_stars=False):
-    log = logging.getLogger('modmap')
+    log = logging.getLogger('kameris')
     if start_stars:
         step_format = '*** %s %s'
     else:

samples/settings.yml

@@ -13,7 +13,7 @@ local_dirs:
 #remote_logging:
 #  # only AWS CloudWatch is currently supported
 #  destination: cloudwatch
-#  log_group: modmap # the CloudWatch group (must already exist)
+#  log_group: kameris # the CloudWatch group (must already exist)
 #  region: us-east-1 # the AWS region
 #  aws_key: # your AWS Access Key ID
 #  aws_secret: # your AWS Secret Access Key