doc: minor fixes

docs/source/cli/index.rst

@@ -97,6 +97,6 @@ Contents
 
 ----
 
-.. click:: momics.cli:cli
+.. click:: momics.cli.cli:cli
   :prog: momics
   :nested: full

src/momics/chromnn.py

@@ -10,16 +10,11 @@
 class ChromNN:
     """
     This class implements a convolutional neural network for the prediction of
-    chromatin modality from another modality. The model implements a series of
+    chromatin modality from another modality. The model consists of a series of
     convolutional blocks with residual connections and dropout layers.
-
-    Attributes
-    ----------
     """
 
     def __init__(self, input=DEFAULT_CHROMNN_INPUT_LAYER, output=DEFAULT_CHROMNN_OUTPUT_LAYER) -> None:
-        """ """
-
         kernel_init = tf.keras.initializers.VarianceScaling()
 
         # First convolutional block

src/momics/cli/tree.py

@@ -15,24 +15,32 @@
 def tree(ctx, path):
     """List all the TileDB tables already ingested."""
 
-    mom = m.Momics(path)
-    chrs = mom.chroms()["chrom"]
-
     if path.endswith("/"):
         name = Path(os.path.dirname(path)).with_suffix("").name
     else:
         name = Path(path).with_suffix("").name
 
-    vfs = mom.cfg.vfs
-    chroms_uri = mom._build_uri("genome", "chroms") + ".tdb"
-    sequence_uri = mom._build_uri("genome", chrs[0]) + ".tdb"
-    tracks_uri = mom._build_uri("coverage", "tracks") + ".tdb"
-    features_uri = mom._build_uri("annotations", "features") + ".tdb"
+    mom = m.Momics(path)
+    chrs = mom.chroms()["chrom"]
+
+    if chrs.empty:
+        has_chroms = False
+        has_seq = False
+        has_tracks = False
+        has_features = False
+
+    else:
+        has_chroms = True
+
+        vfs = mom.cfg.vfs
+        chroms_uri = mom._build_uri("genome", "chroms") + ".tdb"
+        sequence_uri = mom._build_uri("genome", chrs[0]) + ".tdb"
+        tracks_uri = mom._build_uri("coverage", "tracks") + ".tdb"
+        features_uri = mom._build_uri("annotations", "features") + ".tdb"
 
-    has_chroms = vfs.is_dir(chroms_uri)
-    has_seq = vfs.is_dir(sequence_uri)
-    has_tracks = vfs.is_dir(tracks_uri)
-    has_features = vfs.is_dir(features_uri)
+        has_seq = vfs.is_dir(sequence_uri)
+        has_tracks = vfs.is_dir(tracks_uri)
+        has_features = vfs.is_dir(features_uri)
 
     if has_chroms:
         print("\u2714 Chromosomes registered")

src/momics/dataset.py

@@ -18,9 +18,8 @@ class MomicsDataset(tf.data.Dataset):
     For a more basic generator to stream a `momics` by batches of ranges,
     see `momics.streamer.MomicsStreamer`.
 
-    See Also
-    --------
-        `momics.streamer.MomicsStreamer`
+    See Also:
+        :class:`momics.streamer.MomicsStreamer`
     """
 
     def __new__(

src/momics/momics.py

@@ -59,10 +59,23 @@ class Momics:
     """
     A class to manipulate `.momics` repositories.
 
-    Attributes
-    ----------
-    path : str
-        Path to a `.momics` repository.
+    `.momics` repositories are a TileDB-backed storage system for genomics data.
+    They are structured as follows:
+
+    - `./genome/chroms.tdb` - table for ingested chromosomes;
+    - `./coverage/tracks.tdb` - table for ingested bigwig tracks;
+    - `./annotations/features.tdb` - table for ingested feature sets.
+
+    In each subdirectory, there is also one `.tdb` file per chromosome, which
+    stores the following data:
+
+    - In `./genome/{X}.tdb`: the reference sequence of the chromosome;
+    - In `./coverage/{X}.tdb`: the coverage scores of the chromosome;
+    - In `./annotations/{X}.tdb`: the genomic features of the chromosome.
+
+    Attributes:
+        path (str): Path to a `.momics` repository.
+        cfg (MomicsConfig): Configuration object.
     """
 
     def __init__(
@@ -85,7 +98,7 @@ def __init__(
         self.cfg = config
 
         ## Check if folder exists. If not, create it.
-        if not self.cfg.vfs.is_dir(self.path):
+        if not utils._repo_exists(self.path, self.cfg):
             self.cfg.vfs.create_dir(self.path)
             self._create_repository()
             logger.info(f"Created {self.path}")
@@ -879,7 +892,7 @@ def remove_directory_until_success(vfs, dir_uri, max_retries=10, retry_delay=2):
         return True
 
     def export_track(self, track: str, output: Path) -> "Momics":
-        """Export a track from a `.momics` repository as a `.bw `file.
+        """Export a track from a `.momics` repository as a `.bw` file.
 
         Args:
             track (str): Which track to remove
@@ -908,10 +921,10 @@ def export_track(self, track: str, output: Path) -> "Momics":
         return self
 
     def export_sequence(self, output: Path) -> "Momics":
-        """Export sequence from a `.momics` repository as a `.fa `file.
+        """Export sequence from a `.momics` repository as a `.fa` file.
 
         Args:
-            output (Path): Prefix of the output bigwig file
+            output (Path): Prefix of the output fasta file
 
         Returns:
             Momics: An updated Momics object
@@ -933,7 +946,7 @@ def export_sequence(self, output: Path) -> "Momics":
         return self
 
     def export_features(self, features: str, output: Path) -> "Momics":
-        """Export a features set from a `.momics` repository as a `.bed `file.
+        """Export a features set from a `.momics` repository as a `.bed` file.
 
         Args:
             features (str): Which features to remove

src/momics/momicsquery.py

@@ -22,14 +22,13 @@
 class MomicsQuery:
     """A class to query `.momics` repositories.
 
-    Attributes
-    ----------
-    momics (Momics): a local `.momics` repositoryasdcasdc.
-    queries (dict): Dict. of pr.PyRanges object.
-    coverage (dict): Dictionary of coverage scores extracted from the \
-        `.momics` repository, populated after calling `q.query_tracks()`
-    seq (dict): Dictionary of sequences extracted from the `.momics` \
-        repository, populated after calling `q.query_seq()`
+    Attributes:
+        momics (Momics): a local `.momics` repository.
+        queries (pr.PyRanges): `pr.PyRanges` object
+        coverage (dict): Dictionary of coverage scores extracted from the \
+            `.momics` repository, populated after calling `q.query_tracks()`
+        seq (dict): Dictionary of sequences extracted from the `.momics` \
+            repository, populated after calling `q.query_seq()`
     """
 
     def __init__(self, momics: Momics, bed: pr.PyRanges):

src/momics/streamer.py

@@ -17,17 +17,15 @@ class MomicsStreamer:
 
     For a tensorflow DataSet constructor, see `momics.dataset.MomicsDataset`.
 
-    See Also
-    --------
-        `momics.dataset.MomicsDataset`
-
-    Attributes
-    ----------
-    momics (Momics): a local `.momics` repository.
-    ranges (dict): pr.PyRanges object.
-    batch_size (int): the batch size
-    features (list): list of track labels to query
-    silent (bool): whether to suppress info messages
+    See Also:
+        :class:`momics.dataset.MomicsDataset`
+
+    Attributes:
+        momics (Momics): a local `.momics` repository.
+        ranges (dict): pr.PyRanges object.
+        batch_size (int): the batch size
+        features (list): list of track labels to query
+        silent (bool): whether to suppress info messages
     """
 
     def __init__(

src/momics/utils.py

@@ -8,6 +8,14 @@
 import pyfaidx
 
 
+def _repo_exists(path, cfg) -> bool:
+    x = cfg.vfs.is_dir(path)
+    if x:
+        return True
+    else:
+        return False
+
+
 def _check_fasta_lengths(fasta, chroms) -> None:
     reference_lengths = dict(zip(chroms["chrom"], chroms["length"]))
     if isinstance(fasta, Path):