Split out reports dependencies

.circleci/config.yml

@@ -13,17 +13,17 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py38-v2-{{ checksum "pyproject.toml" }}
+          key: conda-py38-v3-{{ checksum "pyproject.toml" }}
       - run:
           name: Generate environment
           command: |
             if [ ! -d /opt/conda/envs/tedana_py38 ]; then
               conda create -yq -n tedana_py38 python=3.8
               source activate tedana_py38
-              pip install -e .[tests]
+              pip install -e .[reports,tests]
             fi
       - save_cache:
-          key: conda-py38-v2-{{ checksum "pyproject.toml" }}
+          key: conda-py38-v3-{{ checksum "pyproject.toml" }}
           paths:
             - /opt/conda/envs/tedana_py38
 
@@ -34,7 +34,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py38-v2-{{ checksum "pyproject.toml" }}
+          key: conda-py38-v3-{{ checksum "pyproject.toml" }}
       - run:
           name: Running unit tests
           command: |
@@ -56,7 +56,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py39-v2-{{ checksum "pyproject.toml" }}
+          key: conda-py39-v3-{{ checksum "pyproject.toml" }}
       - run:
           name: Generate environment
           command: |
@@ -65,7 +65,7 @@ jobs:
             if [ ! -d /opt/conda/envs/tedana_py39 ]; then
               conda create -yq -n tedana_py39 python=3.9
               source activate tedana_py39
-              pip install .[tests]
+              pip install .[reports,tests]
             fi
       - run:
           name: Running unit tests
@@ -75,7 +75,7 @@ jobs:
             mkdir /tmp/src/coverage
             mv /tmp/src/tedana/.coverage /tmp/src/coverage/.coverage.py39
       - save_cache:
-          key: conda-py39-v2-{{ checksum "pyproject.toml" }}
+          key: conda-py39-v3-{{ checksum "pyproject.toml" }}
           paths:
             - /opt/conda/envs/tedana_py39
       - persist_to_workspace:
@@ -99,7 +99,7 @@ jobs:
             if [ ! -d /opt/conda/envs/tedana_py310 ]; then
               conda create -yq -n tedana_py310 python=3.10
               source activate tedana_py310
-              pip install .[tests]
+              pip install .[reports,tests]
             fi
       - run:
           name: Running unit tests
@@ -192,7 +192,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py38-v2-{{ checksum "pyproject.toml" }}
+          key: conda-py38-v3-{{ checksum "pyproject.toml" }}
       - run:
           name: Style check
           command: |
@@ -208,7 +208,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py38-v2-{{ checksum "pyproject.toml" }}
+          key: conda-py38-v3-{{ checksum "pyproject.toml" }}
       - run:
           name: Run integration tests
           no_output_timeout: 40m
@@ -233,7 +233,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py38-v2-{{ checksum "pyproject.toml" }}
+          key: conda-py38-v3-{{ checksum "pyproject.toml" }}
       - run:
           name: Run integration tests
           no_output_timeout: 40m
@@ -258,7 +258,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py38-v2-{{ checksum "pyproject.toml" }}
+          key: conda-py38-v3-{{ checksum "pyproject.toml" }}
       - run:
           name: Run integration tests
           no_output_timeout: 40m
@@ -283,7 +283,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py38-v2-{{ checksum "pyproject.toml" }}
+          key: conda-py38-v3-{{ checksum "pyproject.toml" }}
       - run:
           name: Run integration tests
           no_output_timeout: 40m
@@ -308,7 +308,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py38-v2-{{ checksum "pyproject.toml" }}
+          key: conda-py38-v3-{{ checksum "pyproject.toml" }}
       - run:
           name: Run integration tests
           no_output_timeout: 40m
@@ -335,7 +335,7 @@ jobs:
           at: /tmp
       - checkout
       - restore_cache:
-          key: conda-py38-v2-{{ checksum "pyproject.toml" }}
+          key: conda-py38-v3-{{ checksum "pyproject.toml" }}
       - run:
           name: Merge coverage files
           command: |

pyproject.toml

@@ -21,7 +21,6 @@ classifiers = [
 license = {file = "LICENSE"}
 requires-python = ">=3.8"
 dependencies = [
-    "bokeh>=1.0.0,<=3.4.1",
     "mapca>=0.0.4,<=0.0.5",
     "matplotlib",
     "nibabel>=2.5.1,<=5.2.1",
@@ -50,7 +49,9 @@ doc = [
     "sphinx-argparse",
     "sphinxcontrib-bibtex",
 ]
-
+reports = [
+    "bokeh>=1.0.0,<=3.4.1",
+]
 tests = [
     "codecov",
     "coverage",
@@ -69,7 +70,7 @@ tests = [
 ]
 
 # Aliases
-all = ["tedana[dev,doc,tests]"]
+all = ["tedana[dev,doc,reports,tests]"]
 
 [project.scripts]
 ica_reclassify = "tedana.workflows.ica_reclassify:_main"

tedana/reporting/dynamic_figures.py

@@ -4,7 +4,6 @@
 
 import numpy as np
 import pandas as pd
-from bokeh import events, models, plotting, transform
 from sklearn.preprocessing import MinMaxScaler
 
 color_mapping = {"accepted": "#2ecc71", "rejected": "#e74c3c", "ignored": "#3498db"}
@@ -67,6 +66,8 @@ def _create_data_struct(comptable_path, color_mapping=color_mapping):
     cds : bokeh.models.ColumnDataSource
         Data structure with all the fields to plot or hover over
     """
+    from bokeh import models
+
     unused_cols = [
         "normalized variance explained",
         "countsigFT2",
@@ -152,6 +153,8 @@ def _create_kr_plt(comptable_cds, kappa_elbow=None, rho_elbow=None):
     fig : bokeh.plotting.figure.Figure
         Bokeh scatter plot of kappa vs. rho
     """
+    from bokeh import models, plotting
+
     # Create Panel for the Kappa - Rho Scatter
     kr_hovertool = models.HoverTool(
         tooltips=[
@@ -272,6 +275,8 @@ def _create_sorted_plt(
     fig : bokeh.plotting.figure.Figure
         Bokeh plot of components ranked by a given feature
     """
+    from bokeh import models, plotting
+
     hovertool = models.HoverTool(
         tooltips=[
             ("Component ID", "@component"),
@@ -324,6 +329,7 @@ def _create_sorted_plt(
 
 
 def _create_varexp_pie_plt(comptable_cds):
+    from bokeh import models, plotting, transform
 
     pie_hovertool = models.HoverTool(
         tooltips=[
@@ -383,6 +389,8 @@ def _tap_callback(comptable_cds, div_content, io_generator):
     CustomJS : bokeh.models.CustomJS
         Javascript function that adds the tapping functionality
     """
+    from bokeh import models
+
     return models.CustomJS(
         args=dict(
             source_comp_table=comptable_cds,
@@ -419,5 +427,7 @@ def _link_figures(fig, comptable_ds, div_content, io_generator):
         Same as input figure, but with a linked method to
         its Tap event.
     """
+    from bokeh import events
+
     fig.js_on_event(events.Tap, _tap_callback(comptable_ds, div_content, io_generator))
     return fig

tedana/reporting/html_report.py

@@ -8,8 +8,6 @@
 from string import Template
 
 import pandas as pd
-from bokeh import __version__ as bokehversion
-from bokeh import embed, layouts, models
 from pybtex.database.input import bibtex
 from pybtex.plugin import find_plugin
 
@@ -189,6 +187,8 @@ def _save_as_html(body):
     body : str
         Body for HTML report with embedded figures
     """
+    from bokeh import __version__ as bokehversion
+
     resource_path = Path(__file__).resolve().parent.joinpath("data", "html")
     head_template_name = "report_head_template.html"
     head_template_path = resource_path.joinpath(head_template_name)
@@ -238,6 +238,8 @@ def generate_report(io_generator: OutputGenerator) -> None:
     -----
     This writes out an HTML report to a file.
     """
+    from bokeh import embed, layouts, models
+
     # Load the component time series
     comp_ts_path = io_generator.get_name("ICA mixing tsv")
     comp_ts_df = pd.read_csv(comp_ts_path, sep="\t", encoding="utf=8")

tedana/utils.py

@@ -8,19 +8,9 @@
 
 import nibabel as nib
 import numpy as np
-from bokeh import __version__ as bokeh_version
-from mapca import __version__ as mapca_version
-from matplotlib import __version__ as matplotlib_version
-from nibabel import __version__ as nibabel_version
-from nilearn import __version__ as nilearn_version
 from nilearn._utils import check_niimg
-from numpy import __version__ as numpy_version
-from pandas import __version__ as pandas_version
-from scipy import __version__ as scipy_version
 from scipy import ndimage
-from sklearn import __version__ as sklearn_version
 from sklearn.utils import check_array
-from threadpoolctl import __version__ as threadpoolctl_version
 
 LGR = logging.getLogger("GENERAL")
 RepLGR = logging.getLogger("REPORT")
@@ -555,9 +545,22 @@
     return op.abspath(op.join(op.dirname(__file__), "resources") + op.sep)
 
 
+def _check_report_dependencies():
+    """Check if dependencies required for reports are installed."""
+    try:
+        import bokeh  # noqa F401
+        import jinja2  # noqa F401
+    except ImportError:
+        raise ImportError(
+            "Running tedana/ica_reclassify without the --no-reports flag requires extra "
+            "dependencies. "
+            "Please install tedana with the [reports] dependency group "
+            "(e.g., 'pip install tedana[reports]')."
+        )
+
+
 def get_system_version_info():
-    """
-    Return information about the system tedana is being run on.
+    """Return information about the system tedana is being run on.
 
     Returns
     -------
@@ -566,10 +569,19 @@
         and python and python library versioning info for key
         modules used by tedana.
     """
+    from mapca import __version__ as mapca_version
+    from matplotlib import __version__ as matplotlib_version
+    from nibabel import __version__ as nibabel_version
+    from nilearn import __version__ as nilearn_version
+    from numpy import __version__ as numpy_version
+    from pandas import __version__ as pandas_version
+    from scipy import __version__ as scipy_version
+    from sklearn import __version__ as sklearn_version
+    from threadpoolctl import __version__ as threadpoolctl_version
+
     system_info = platform.uname()
 
     python_libraries = {
-        "bokeh": bokeh_version,
         "matplotlib": matplotlib_version,
         "mapca": mapca_version,
         "nibabel": nibabel_version,
@@ -581,6 +593,13 @@
         "threadpoolctl": threadpoolctl_version,
     }
 
+    try:
+        from bokeh import __version__ as bokeh_version
+
+        python_libraries["bokeh"] = bokeh_version
+    except ImportError:
+        pass
+
     return {
         "System": system_info.system,
         "Node": system_info.node,

tedana/workflows/ica_reclassify.py

@@ -247,18 +247,17 @@ def ica_reclassify_workflow(
     quiet=False,
     reclassify_command=None,
 ):
-    """
-    Run the post-tedana manual classification workflow.
+    """Run the post-tedana manual classification workflow.
 
     Please remember to cite [1]_.
 
     Parameters
     ----------
     registry : :obj:`str`
         The previously run registry as a JSON file.
-    accept : :obj: `list`
+    accept : :obj:`list`
         A list of integer values of components to accept in this workflow.
-    reject : :obj: `list`
+    reject : :obj:`list`
         A list of integer values of components to reject in this workflow.
     out_dir : :obj:`str`, optional
         Output directory.
@@ -267,10 +266,10 @@ def ica_reclassify_workflow(
         denoising. Default is False.
     mir : :obj:`bool`, optional
         Run minimum image regression after denoising. Default is False.
-    no_reports : obj:'bool', optional
+    no_reports : obj:`bool`, optional
         Do not generate .html reports and .png plots. Default is false such
         that reports are generated.
-    png_cmap : obj:'str', optional
+    png_cmap : obj:`str`, optional
         Name of a matplotlib colormap to be used when generating figures.
         Cannot be used with --no-png. Default is 'coolwarm'.
     debug : :obj:`bool`, optional
@@ -298,6 +297,9 @@ def ica_reclassify_workflow(
            TE-dependent analysis of multi-echo fMRI with tedana.
            Journal of Open Source Software, 6(66), 3669. doi:10.21105/joss.03669.
     """
+    if not no_reports:
+        utils._check_report_dependencies()
+
     out_dir = op.abspath(out_dir)
     if not op.isdir(out_dir):
         os.mkdir(out_dir)

tedana/workflows/tedana.py

@@ -460,6 +460,9 @@ def tedana_workflow(
     ----------
     .. footbibliography::
     """
+    if not no_reports:
+        utils._check_report_dependencies()
+
     out_dir = op.abspath(out_dir)
     if not op.isdir(out_dir):
         os.mkdir(out_dir)