refactoring

Dockerfile

@@ -1,7 +1,7 @@
 FROM python:3.11.3-slim
 
 ADD *.py /usr/local/bin/
-ADD src /usr/local/bin/src
-ADD src/utils /usr/local/bin/src/utils
+ADD cami_amber /usr/local/bin/cami_amber
+ADD cami_amber/utils /usr/local/bin/cami_amber/utils
 ADD requirements.txt requirements.txt
 RUN pip install -r requirements.txt

amber.py

@@ -15,6 +15,15 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
+from cami_amber import amber_html
+from cami_amber import plot_by_genome
+from cami_amber import plots
+from cami_amber.utils import load_data
+from cami_amber.utils import argparse_parents
+from cami_amber.utils import labels as utils_labels
+from cami_amber import binning_classes
+from cami_amber.utils import load_ncbi_taxinfo
+from version import __version__
 import argparse
 import errno
 import logging
@@ -23,15 +32,6 @@
 import pandas as pd
 import matplotlib
 matplotlib.use('Agg')
-from src import amber_html
-from src import plot_by_genome
-from src import plots
-from version import __version__
-from src.utils import load_data
-from src.utils import argparse_parents
-from src.utils import labels as utils_labels
-from src import binning_classes
-from src.utils import load_ncbi_taxinfo
 
 
 def get_logger(output_dir, silent):

src/amber_html.py → cami_amber/amber_html.py

@@ -24,10 +24,10 @@
 import logging
 from jinja2 import Template
 from statistics import median
-from src import plots
-from src import binning_classes
-from src.utils import labels as utils_labels
-from src.utils import load_ncbi_taxinfo
+from cami_amber import plots
+from cami_amber import binning_classes
+from cami_amber.utils import labels as utils_labels
+from cami_amber.utils import load_ncbi_taxinfo
 
 import matplotlib
 matplotlib.use('Agg')

src/binning_classes.py → cami_amber/binning_classes.py

@@ -25,12 +25,12 @@
 from abc import ABC, abstractmethod
 from collections import defaultdict
 from collections import OrderedDict
-from src.utils import labels as utils_labels
-from src.utils import load_ncbi_taxinfo
-from src.utils import ProfilingTools as pf
-from src import unifrac_distance as uf
-from src import precision_recall_per_bin
-from src import plots
+from cami_amber.utils import labels as utils_labels
+from cami_amber.utils import load_ncbi_taxinfo
+from cami_amber.utils import ProfilingTools as pf
+from cami_amber import unifrac_distance as uf
+from cami_amber import precision_recall_per_bin
+from cami_amber import plots
 
 
 class Metrics:

src/plot_by_genome.py → cami_amber/plot_by_genome.py

@@ -23,8 +23,8 @@
 currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
 parentdir = os.path.dirname(currentdir)
 sys.path.insert(0, parentdir)
-from src import plots
-from src.utils import labels as utils_labels
+from cami_amber import plots
+from cami_amber.utils import labels as utils_labels
 
 
 def plot_by_genome(data, out_file=None, sort_by='completeness'):

src/plots.py → cami_amber/plots.py

@@ -13,9 +13,9 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
-from src.utils import labels as utils_labels
-from src.utils import load_ncbi_taxinfo
-from src import binning_classes
+from cami_amber.utils import labels as utils_labels
+from cami_amber.utils import load_ncbi_taxinfo
+from cami_amber import binning_classes
 import matplotlib
 matplotlib.use('Agg')
 import seaborn as sns

src/unifrac_distance.py → cami_amber/unifrac_distance.py

@@ -1,6 +1,6 @@
 # This is an example of how to use the script
-from src.utils import ProfilingTools as PF
-from src.utils import EMDUnifrac as EMDU
+from cami_amber.utils import ProfilingTools as PF
+from cami_amber.utils import EMDUnifrac as EMDU
 import numpy as np
 import argparse
 import copy

src/utils/load_data.py → cami_amber/utils/load_data.py

@@ -22,8 +22,8 @@
 from multiprocessing.pool import ThreadPool
 from collections import defaultdict
 from collections import OrderedDict
-from src import binning_classes
-from src.utils import labels as utils_labels
+from cami_amber import binning_classes
+from cami_amber.utils import labels as utils_labels
 
 try:
     import load_ncbi_taxinfo