remove ref constructor and write doc

docs/source/building_splici_index.rst

@@ -1,5 +1,5 @@
 #################################################################################
-(Deprecated since v0.10.0)Preparing an expanded transcriptome reference for quantification with alevin-fry
+(Deprecated since v0.10.0) Preparing an expanded transcriptome reference for quantification with alevin-fry
 #################################################################################
 
 The USA mode in alevin-fry requires an expanded index reference, in which sequences represent spliced and unspliced transcripts. Pyroe provides CLI programs and python functions to build the pre-defined expanded references, the spliced + intronic (*splici*) reference, which includes the spliced transcripts plus the (merged and collapsed) intronic sequences of each gene and the spliced + unspliced (*spliceu*) reference, which consists of the spliced transcripts plus the unspliced transcript (genes' entire genomic interval) of each gene. The ``make_splici_txome()`` and ``make_spliceu_txome()`` python functions are designed to make the *splici* and *spliceu* reference by taking a genome FASTA file and a gene annotation GTF file as the input. Furthermore, the 

docs/source/geneid_to_name.rst

@@ -1,4 +1,4 @@
-(Deprecated since v0.10.0)Generating a gene id to gene name mapping
+(Deprecated since v0.10.0) Generating a gene id to gene name mapping
 =========================================
 
 It is often useful to perform analyses with gene *names* rather than gene *identifiers*. The `convert <https://pyroe.readthedocs.io/en/latest/converting_quants.html>`_ command of ``pyroe`` allows you to specify an id to name mapping so that the converted output matrix will be labeled with gene names rather than identifiers.  However, you must provide it with a 2-column tab-separated file mapping IDs to names.  This command can help you with that task.

docs/source/index.rst

@@ -4,9 +4,12 @@ Welcome to the documentation for pyroe
 What is pyroe?
 ===================
 
-The pyroe package provides useful functions for analyzing single-cell or single-nucleus RNA-sequencing data using `alevin-fry`. Since `simpleaf` version 0.14.0, `roers <https://github.com/COMBINE-lab/roers>`_, instead of pyroe, became the default augmented reference constructor for `alevin-fry` and `simpleaf`. Now, the main purpose of `pyroe` is to provide the function `load_fry` to load `alevin-fry` and `simpleaf` quantification results into Python as an `anndata <http://anndata.readthedocs.io/>`_ object, so as to perform downstream analysis provided by `scanpy <https://scanpy.readthedocs.io/en/stable/index.html>`_.
+The pyroe package provides useful functions for analyzing single-cell or single-nucleus RNA-sequencing data using `alevin-fry`.
+The main purpose of `pyroe` is to provide the function `load_fry` to load `alevin-fry` and `simpleaf` quantification results into Python as an `anndata <http://anndata.readthedocs.io/>`_ object, so as to perform downstream analysis provided by `scanpy <https://scanpy.readthedocs.io/en/stable/index.html>`_. Moreover, `pyroe` also provides functions to fetch the pre-computed quantification results from the `quantaf <https://combine-lab.github.io/quantaf/>`_ database. 
 
-Although pyroe is available on bioconda and can be easily installed, if you encounter any problem during installation, you can also define the `load_fry` function locally in your python script by copying the function definition defined `here <https://github.com/COMBINE-lab/pyroe/blob/main/src/pyroe/load_fry.py>`_. The only dependency of `load_fry` is `scanpy <https://scanpy.readthedocs.io/en/stable/installation.html>`_. 
+In previous versions (before v 0.10.0), pyroe also provided the functions to construct the augmented transcriptome references. Since `simpleaf` version 0.14.0, `roers <https://github.com/COMBINE-lab/roers>`_, instead of pyroe, became the default augmented reference constructor for `alevin-fry` and `simpleaf`. If you would like to use the deprecated functions to construct the augmented references, please install an older version of pyroe. Notice that old versions of pyroe are compatitble with pandas version less than 2.0.0. So, we suggest you to install the old versions of pyroe in a conda environment with a isolated environment, so as to not affect the other packages in your system.  
+
+**To note that** although pyroe is available on bioconda and can be easily installed, if you encounter any problem during installation, you can define the `load_fry` function locally in your python script by copying the function definition defined `here <https://github.com/COMBINE-lab/pyroe/blob/main/src/pyroe/load_fry.py>`_. The only dependency of `load_fry` is `scanpy <https://scanpy.readthedocs.io/en/stable/installation.html>`_. 
 
 Additionally, 
 

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = pyroe
-version = 0.9.3
+version = 0.10.0
 author = Dongze He, Rob Patro
 author_email = dhe17@umd.edu, rob@cs.umd.edu
 description = utilities of alevin-fry

src/pyroe/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.9.3"
+__version__ = "0.10.0"
 
 from pyroe.load_fry import load_fry
 from pyroe.fetch_processed_quant import fetch_processed_quant
@@ -12,8 +12,8 @@
 #     from pyroe.make_txome import make_splici_txome, make_spliceu_txome
 #     from pyroe.id_to_name import id_to_name
 # except ImportError:
-#     make_splici_txome = None 
-#     make_spliceu_txome = None 
-#     id_to_name = None 
+#     make_splici_txome = None
+#     make_spliceu_txome = None
+#     id_to_name = None
 
 # flake8: noqa