readme/docs organization

jkmckenna · jkmckenna · commit 19e32c9887e5 · 2026-01-09T10:16:08.000-08:00
diff --git a/README.md b/README.md
@@ -12,22 +12,3 @@ The following CLI tools need to be installed and configured before using the inf
 1) [Dorado](https://github.com/nanoporetech/dorado) -> Basecalling, alignment, demultiplexing. Required for Nanopore SMF experiments, but not Illumina SMF experiments.
 2) [Minimap2](https://github.com/lh3/minimap2) -> Aligner if not using dorado. Support for other aligners could eventually be added if needed.
 3) [Modkit](https://github.com/nanoporetech/modkit) -> Extracting read level methylation metrics from the MM/ML tags in BAM files. Only required for direct modification detection SMF protocols.
-
-## Announcements
-
-### 12/02/25 - Version 0.2.3 is available through PyPI
-Version 0.2.3 provides the core smftools functionality through several command line commands (load, preprocess, spatial, hmm).
-
-### 11/05/25 - Version 0.2.1 is available through PyPI
-Version 0.2.1 makes the core workflow (smftools load) a command line tool that takes in an experiment_config.csv file for input/output and parameter management.
-
-### 05/29/25 - Version 0.1.6 is available through PyPI.
-Informatics, preprocessing, tools, plotting modules have core functionality that is approaching stability on MacOS(Intel/Silicon) and Linux(Ubuntu). I will work on improving documentation/tutorials shortly. The base PyTorch/Scikit-Learn ML-infrastructure is going through some organizational changes to work with PyTorch Lightning, Hydra, and WanDB to facilitate organizational scaling, multi-device usage, and logging.
-
-### 10/01/24 - More recent versions are being updated frequently. Installation from source over PyPI is recommended!
-
-### 09/09/24 - The version 0.1.1 package ([smftools-0.1.1](https://pypi.org/project/smftools/)) is installable through pypi!
-The informatics module has been bumped to alpha-phase status. This module can deal with POD5s and unaligned BAMS from nanopore conversion and direct SMF experiments, as well as FASTQs from Illumina conversion SMF experiments. Primary output from this module is an AnnData object containing all relevant SMF data, which is compatible with all downstream smftools modules. The other modules are still in pre-alpha phase. Preprocessing, Tools, and Plotting modules should be promoted to alpha-phase within the next month or so.
-
-### 08/30/24 - The version 0.1.0 package ([smftools-0.1.0](https://pypi.org/project/smftools/)) is installable through pypi!
-Currently, this package (smftools-0.1.0) is going through rapid improvement (dependency handling accross Linux and Mac OS, testing, documentation, debugging) and is still too early in development for widespread use. The underlying functionality was originally developed as a collection of scripts for single molecule footprinting (SMF) experiments in our lab, but is being packaged/developed to facilitate the expansion of SMF to any lab that is interested in performing these styles of experiments/analyses. The alpha-phase package is expected to be available within a couple months, so stay tuned!
diff --git a/docs/source/basic_usage.md b/docs/source/basic_usage.md
@@ -13,7 +13,7 @@ This command takes a user passed config file handling:
     - Experiment info (SMF modality, sequencer type, barcoding kit if nanopore, sample sheet with metadata mapping)
     - Options to override default workflow parameters from smftools/config. Params are handled from default.yaml -> modality_type.yaml -> user passed config.csv.
 
-![](docs/source/_static/smftools_informatics_diagram.png)
+![](_static/smftools_informatics_diagram.png)
 
 ## Preprocess Usage
 
@@ -23,7 +23,7 @@ This command performs preprocessing on the anndata object. It automatically runs
 smftools preprocess "/Path_to_experiment_config.csv"
 ```
 
-![](docs/source/_static/smftools_preprocessing_diagram.png)
+![](_static/smftools_preprocessing_diagram.png)
 
 ## Spatial Usage
 
diff --git a/docs/source/release-notes/0.1.0.md b/docs/source/release-notes/0.1.0.md
@@ -1,4 +1,5 @@
 (v0.1.0)=
 
 0.1.0 2024-08-30
-smftools initial release. Pre-Alpha phase. J McKenna
+smftools initial release. Pre-Alpha phase. J McKenna
+Currently, this package (smftools-0.1.0) is going through rapid improvement (dependency handling accross Linux and Mac OS, testing, documentation, debugging) and is still too early in development for widespread use. The underlying functionality was originally developed as a collection of scripts for single molecule footprinting (SMF) experiments in our lab, but is being packaged/developed to facilitate the expansion of SMF to any lab that is interested in performing these styles of experiments/analyses. The alpha-phase package is expected to be available within a couple months, so stay tuned!
diff --git a/docs/source/release-notes/0.1.1.md b/docs/source/release-notes/0.1.1.md
@@ -0,0 +1,4 @@
+(v0.1.1)=
+
+0.1.1 2024-09-09
+The informatics module has been bumped to alpha-phase status. This module can deal with POD5s and unaligned BAMS from nanopore conversion and direct SMF experiments, as well as FASTQs from Illumina conversion SMF experiments. Primary output from this module is an AnnData object containing all relevant SMF data, which is compatible with all downstream smftools modules. The other modules are still in pre-alpha phase. Preprocessing, Tools, and Plotting modules should be promoted to alpha-phase within the next month or so.
diff --git a/docs/source/release-notes/0.1.6.md b/docs/source/release-notes/0.1.6.md
@@ -0,0 +1,4 @@
+(v0.1.6)=
+
+0.1.6 2025-05-29
+Informatics, preprocessing, tools, plotting modules have core functionality that is approaching stability on MacOS (Intel/Silicon) and Linux (Ubuntu). Documentation/tutorials are still being improved. The base PyTorch/Scikit-Learn ML-infrastructure is going through organizational changes to work with PyTorch Lightning, Hydra, and WanDB to facilitate scaling, multi-device usage, and logging.
diff --git a/docs/source/release-notes/0.2.1.md b/docs/source/release-notes/0.2.1.md
@@ -0,0 +1,4 @@
+(v0.2.1)=
+
+0.2.1 2025-11-05
+Version 0.2.1 makes the core workflow (smftools load) a command line tool that takes in an experiment_config.csv file for input/output and parameter management.
diff --git a/docs/source/release-notes/0.2.3.md b/docs/source/release-notes/0.2.3.md
@@ -0,0 +1,4 @@
+(v0.2.3)=
+
+0.2.3 2025-12-02
+Version 0.2.3 provides the core smftools functionality through several command line commands (load, preprocess, spatial, hmm).
diff --git a/src/smftools/preprocessing/binary_layers_to_ohe.py b/src/smftools/preprocessing/binary_layers_to_ohe.py
@@ -4,6 +4,7 @@
 
 logger = get_logger(__name__)
 
+
 ## Conversion SMF Specific
 def binary_layers_to_ohe(adata, binary_layers, stack="hstack"):
     """
diff --git a/src/smftools/preprocessing/calculate_position_Youden.py b/src/smftools/preprocessing/calculate_position_Youden.py
@@ -3,6 +3,8 @@
 from smftools.logging_utils import get_logger
 
 logger = get_logger(__name__)
+
+
 def calculate_position_Youden(
     adata,
     positive_control_sample=None,
diff --git a/src/smftools/preprocessing/calculate_read_length_stats.py b/src/smftools/preprocessing/calculate_read_length_stats.py
@@ -4,6 +4,7 @@
 
 logger = get_logger(__name__)
 
+
 # Read length QC
 def calculate_read_length_stats(adata, reference_column="", sample_names_col=""):
     """
diff --git a/src/smftools/preprocessing/filter_reads_on_length_quality_mapping.py b/src/smftools/preprocessing/filter_reads_on_length_quality_mapping.py
@@ -8,6 +8,7 @@
 
 logger = get_logger(__name__)
 
+
 def filter_reads_on_length_quality_mapping(
     adata: ad.AnnData,
     filter_on_coordinates: Union[bool, Sequence] = False,
@@ -99,9 +100,7 @@ def _coerce_range(range_arg):
     # read length filter
     if (rl_min is not None) or (rl_max is not None):
         if "mapped_length" not in adata_work.obs.columns:
-            logger.warning(
-                "'mapped_length' not found in adata.obs — skipping read_length filter."
-            )
+            logger.warning("'mapped_length' not found in adata.obs — skipping read_length filter.")
         else:
             vals = pd.to_numeric(adata_work.obs["mapped_length"], errors="coerce")
             mask = pd.Series(True, index=adata_work.obs.index)
diff --git a/src/smftools/preprocessing/filter_reads_on_modification_thresholds.py b/src/smftools/preprocessing/filter_reads_on_modification_thresholds.py
@@ -9,6 +9,7 @@
 
 logger = get_logger(__name__)
 
+
 def filter_reads_on_modification_thresholds(
     adata: ad.AnnData,
     smf_modality: str,
diff --git a/src/smftools/preprocessing/make_dirs.py b/src/smftools/preprocessing/make_dirs.py
@@ -4,6 +4,7 @@
 
 logger = get_logger(__name__)
 
+
 # General
 def make_dirs(directories):
     """
