update setup.py and CHANGELOG

CHANGELOG.md

@@ -1,8 +1,9 @@
 * LAML version 0.0.4
+    * add functionalities to create character matrices from fastq files (borrowed from a module of Cassiopeia) 
     * handle mismatch between character matrix and prior pickle
     * fix error in doing topology search on multiple input trees
     * more informative messages on handling polytomies
-* LAML version 0.0.3 (depricated)
+* LAML version 0.0.3 (deprecated)
     * attempt to allow user-specified sampling times
     * seems to work for branch length estimation on a fixed topology, but fails on doing topology search
     * roll-back to the previous version

run_laml.py

@@ -40,7 +40,7 @@ def main():
     parser._action_groups.append(otherOptions)
 
     # input arguments
-    requiredNamed.add_argument("-t","--topology",required=True,help="[REQUIRED] Binary input tree topology in newick format. Branch lengths will be ignored.") 
+    requiredNamed.add_argument("-t","--topology",required=True,help="[REQUIRED] The input tree topology in newick format. Branch lengths will be ignored.") 
     requiredNamed.add_argument("-c","--characters",required=True,help="[REQUIRED] The input character matrix. Must have header.")
 
     inputOptions.add_argument("-p","--priors",required=False, default="uniform", help="The input prior matrix Q. Default: if not specified, use a uniform prior.")

setup.py

@@ -17,6 +17,12 @@ def recursive_list_dir(path):
                 listing.append(z.split(path+'/')[1])
     return listing
 
+# Note from GC
+    # 1. If installing from python setup.py install, please `pip install cvxpy` first. 
+    # 2. SCS requires numpy < 1.2 to be installed: https://github.com/bodono/scs-python/issues/32#issuecomment-802977693
+    # 3. cvxpy fails to install on python 3.12, requires SCS, ECOS and OSQP: https://github.com/cvxpy/cvxpy/issues/1367
+    # 4. qdldl (dependency of osqp has no wheel for python 3.12): https://github.com/cvxpy/cvxpy/issues/2269
+    # 5. osqp < 0.6.2 does not depend on qdldl to install cvxpy
 
 param = {
         'name': laml_libs.PROGRAM_NAME,
@@ -30,13 +36,8 @@ def recursive_list_dir(path):
         'scripts': ['run_laml.py', 'laml_tests.py', 'extra_laml_tests.py'],
         'zip_safe': True,
         #'setup_requires': ['numpy'],
-        # SCS requires numpy < 1.2 to be installed: https://github.com/bodono/scs-python/issues/32#issuecomment-802977693
-        # cvxpy fails to install on python 3.12, requires SCS, ECOS and OSQP: https://github.com/cvxpy/cvxpy/issues/1367
-        # qdldl (dependency of osqp has no wheel for python 3.12): https://github.com/cvxpy/cvxpy/issues/2269
-        # osqp < 0.6.2 does not depend on qdldl to install cvxpy
-        # NOTE: if installing from python setup.py install, please `pip install cvxpy` first. 
-        'install_requires': ['scipy>=1.3.1', 'cvxpy>=1.4', 'treeswift>=1.1.39', 'Mosek>=10.1.16', 'setuptools'], #, 'treeswift', 'Mosek', 'setuptools', 'scipy==1.11.4', 'scs==3.2.4.post1', 'clarabel==0.7.1'], #'ecos==2.0.13'], #'osqp==0.6.5'], # 'qdldl==0.1.7.post0'], #osqp>=0.6.1', 'ecos>=2', 'clarabel>=0.5.0', 'scs>=3.0', 'cvxpy'],
-        #'install_requires': ['numpy>=1.16', 'treeswift>=1.1.39', 'scipy>=1.3.1', 'cvxpy>=1.4', 'Mosek>=10.1.16', 'cmake>=3.18.0', 'setuptools', 'pybind11'], #'osqp==0.6.1'],
+        'install_requires': ['scipy>=1.3.1', 'cvxpy>=1.4', 'treeswift>=1.1.39', 'Mosek>=10.1.16', 
+                             'Biopython>=1.71','joblib','matplotlib>=2.2.2','setuptools'], 
         'keywords': 'Phylogenetics Evolution Computational Maximum-likelihood Lineage Tracing',
         'long_description': """LAML is a maximum likelihood algorithm under the Probabilistic Mixed-type Missing (PMM) model. Given a lineage tracing experiment character matrix with heterogeneous per-site alphabets and mutation probabilities, LAML will find a maximum likelihood tree topology and estimate branch lengths as well as stochastic dropout and heritable silencing missing data rates.""",
         'classifiers': [