numpy 2 support; update docs

Author: taoliu

ChangeLog

@@ -1,53 +1,59 @@
-2025-02-14  Tao Liu  <[email protected]>
+2025-02-19  Tao Liu  <[email protected]>
 	MACS 3.0.3
 
 	* Features added
 
-	1) FRAG format introduced. FRAG format is for fragment files
-	defined by 10x genomics to store the alignments from single-cell
-	ATAC-seq experiment. It can be regarded as the BEDPE format with
-	two extra columns -- the barcode information and the counts of the
-	fragments aligned to the same location with the same
-	barcode. Currently, `callpeak` and `pileup` both support the new
-	format. We will add support for other functions such as `hmmratac`
-	in the future.
-
-	We implemented the IO module for reading the fragment files in
-	`Parser.FragParser`. And we then implemented a new
-	`PairedEndTrack.PETrackII` to store the data in fragment file,
-	including the barcodes and counts information. In the `PETrackII`
-	class, we are able to extract a subset using a list of barcodes,
-	which enables us to call peaks only on a pool (pseudo-bulk) of
-	cells.
-
-	2) We extensively rewrote the `pyx` codes into `py` codes. In
-	another words, we now apply the 'pure python style' with PEP-484
-	type annotations to our previous Cython style codes. So that, the
-	source codes can be more compatible to Python programming tools
-	such as `flake8`. During rewritting, we cleaned the source codes
-	even more, and removed unnecessary dependencies during
-	compilation. We will continue to do more code cleaning in the
-	future.
-
-	3) We changed the behavior on the usage of 'blacklist' regions in
-	`hmmratac`. We will remove the aligned fragments located in the
-	'blacklist' regions before the EM step to estimate fragment
-	lengths distributions and HMM step to learn and predict nucleosome
-	states. The reason is discussed in #680. To implement this
-	feature, we added the `exclude` functions to PETrackI and
-	PETrackII.
+	1) Now support FRAG format for single-cell ATAC-seq in `callpeak`
+	and `pileup`. FRAG format is used by 10x Genomics to store
+	alignments from the single-cell ATAC-seq pipeline
+	`cellranger-atac` or the multiomics pipeline `cellranger-arc`. The
+	format is essentially BEDPE with two additional columns: the
+	barcode and the count of fragments aligned to the same location
+	with the same barcode. Support for FRAG in other tools is coming
+	soon, as well as for `hmmratac` calls.
+
+	If you specify `-f FRAG` as your input format:
+
+        - You can use a barcode list for a subset of cells with
+	`--barcodes`, then `callpeak` will identify peaks and `pileup`
+	will build pileup track for the fragments of this subset of cells.
+
+	- Duplicates will not get removed as we'll assume all fragments
+	are valid. Optionally, an option, `--max-count`, can be applied to
+	set the maximum count.
+
+	2) We transitioned our `pyx` codes to `py` codes, adopting a 'pure
+	Python style' with PEP-484 type annotations. This change has made
+	oursource codes more compatible with Python programming tools such
+	as `flake8`. During this process, we performed further code
+	cleaning and eliminated unnecessary dependencies. We intend to
+	continue improving our code quality in the future.
+
+	3) We have modified the handling of 'blacklist' regions in the
+	`hmmratac` tool. This change impacts both the
+	Expectation-Maximization (EM) step that estimates fragment length
+	distributions, and the Hidden Markov Model (HMM) step that learns
+	and predicts nucleosome states. We now exclude aligned fragments
+	located in the 'blocklist' regions before both steps. We
+	implemented the `exclude` functions in both PETrackI and PETrackII
+	to support this feature. For more detailed information and the
+	reasoning behind it, refer to issue #680.
+
+	4) We have tested Numpy>=2. Now MACS3 can be run on all Numpy >=
+	1.25.
 
 	* Bug fixed
 
-	1) `hmmratac` option `--keep-duplicate` had opposite effect
-	previously as indicated by the name and description. It has been
-	renamed as `--remove-dup` to reflect the actual
-	behavior. `hmmratac` will not remove duplicated fragments unless
-	this option is set.
+	1) The `hmmratagc` option `--keep-duplicate` previously had the
+	opposite effect of what its name and description
+	suggested. Therefore, it was renamed to `--remove-dup` to more
+	accurately describe the actual behavior. Duplicate fragments will
+	not be removed by `hmmratac` unless this option is explicitly set
+	up.
 
-	2) `hmmratac`: wrong class name used while saving digested signals
-	in BedGraph files. Multiple other issues related to output
-	filenames. #682
+	2) `hmmratac`: wrong class name was used while saving digested
+	signals in BedGraph files. Fixed multiple other issues related to
+	output filenames. #682
 
 	3) Fix issues in big-endian system in `Parser.py` codes. Enable
 	big-endian support in `BAM.py` codes for accessig certain

docs/source/docs/INSTALL.md

@@ -26,7 +26,7 @@ reproducing your results, we also add them into the requirement list
 with specific version numbers. So here is the list of the required
 python libraries that will impact the numerical calculation in MACS3:
 
- - numpy>=1.25 <2.0.0
+ - numpy>=1.25
  - hmmlearn>=0.3.2
  - scikit-learn>=1.3
  - scipy>=1.12

docs/source/index.md

@@ -40,12 +40,13 @@ tools is coming soon, as well as for `hmmratac` calls.
 
 If you specify FRAG as your input format:
 
- - Use a barcode list for a subset of cells and `callpeak` will
-   identify peaks using these fragments.
+ - You can use a barcode list for a subset of cells with `--barcodes`,
+   then `callpeak` will identify peaks and `pileup` will build pileup
+   track for the fragments of this subset of cells.
  - Duplicates will not get removed as we'll assume all fragments are
-   valid. Optionally, an option can be applied to set the maximum
-   count.
-
+   valid. Optionally, an option, `--max-count`, can be applied to set
+   the maximum count.
+ 
 2) We transitioned our `pyx` codes to `py` codes, adopting a 'pure
 Python style' with PEP-484 type annotations. This change has made our
 source codes more compatible with Python programming tools such as
@@ -62,6 +63,8 @@ before both steps. We implemented the `exclude` functions in both
 PETrackI and PETrackII to support this feature. For more detailed
 information and the reasoning behind it, refer to issue #680.
 
+4) We have tested Numpy>=2. Now MACS3 can be run on all Numpy >= 1.25.
+
 ### Bug fixed
 
 1) The `hmmratagc` option `--keep-duplicate` previously had the

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires=['setuptools>=68.0', 'numpy>=1.25,<2', 'scipy>=1.12', 'cykhash>=2.0', 'Cython>=3.0', 'scikit-learn>=1.3', 'hmmlearn>=0.3.2']
+requires=['setuptools>=68.0', 'numpy>=1.25', 'scipy>=1.12', 'cykhash>=2.0', 'Cython>=3.0', 'scikit-learn>=1.3', 'hmmlearn>=0.3.2']
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -25,7 +25,7 @@ classifiers =['Development Status :: 5 - Production/Stable',
               'Programming Language :: Python :: 3.12',
               'Programming Language :: Python :: 3.13',	      
               'Programming Language :: Cython']
-dependencies = ["numpy>=1.25,<2",
+dependencies = ["numpy>=1.25",
 	        "scipy>=1.12",
              	"hmmlearn>=0.3.2",
                 "scikit-learn>=1.3",