From 14a03a7f2b7b1e33f6969d1a97c3f9e4bf032987 Mon Sep 17 00:00:00 2001
From: rob-p <rob.patro@gmail.com>
Date: Fri, 23 Jun 2023 16:34:13 -0400
Subject: [PATCH 1/4] fix: fix bug in format detection for id-to-name

---
 setup.cfg               |  2 +-
 src/pyroe/__init__.py   |  2 +-
 src/pyroe/id_to_name.py | 28 ++++++++++++++++------------
 3 files changed, 18 insertions(+), 14 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index 4fb7b95..8ee6b50 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = pyroe
-version = 0.9.2
+version = 0.9.3
 author = Dongze He, Rob Patro
 author_email = dhe17@umd.edu, rob@cs.umd.edu
 description = utilities of alevin-fry
diff --git a/src/pyroe/__init__.py b/src/pyroe/__init__.py
index ff79848..126c16c 100644
--- a/src/pyroe/__init__.py
+++ b/src/pyroe/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "0.9.2"
+__version__ = "0.9.3"
 
 from pyroe.load_fry import load_fry
 from pyroe.make_txome import make_splici_txome, make_spliceu_txome
diff --git a/src/pyroe/id_to_name.py b/src/pyroe/id_to_name.py
index c29de6a..14c5ad1 100644
--- a/src/pyroe/id_to_name.py
+++ b/src/pyroe/id_to_name.py
@@ -6,31 +6,35 @@
 
 def id_to_name(params):
     format_map = {
-        ".gtf": pyranges.read_gtf,
-        ".gff": pyranges.read_gff3,
-        ".gff3": pyranges.read_gff3,
+        "gtf": pyranges.read_gtf,
+        "gff": pyranges.read_gff3,
+        "gff3": pyranges.read_gff3,
     }
     annot_reader = None
     if params.format is None:
         p = pathlib.Path(params.gtf_file)
-        suffs = [z.lower() for z in p.suffixes]
+        suffs = [z.lower().strip('.') for z in p.suffixes]
 
         z = None
-        if len(suffs) == 1:
-            z = suffs[0]
-        elif len(suffs) == 2 and suffs[-1] == ".gz":
-            z = suffs[-2]
+        if len(suffs) >= 1:
+            # look at the final suffix
+            z = suffs[-1]
+            # if the final suffix is gz and there are 
+            # suffixes preceding it, check the penultimate
+            # one and use that
+            if z == "gz" and len(suffs) > 1:
+                z = suffs[-2]
 
-        if z in format_map.keys():
-            annot_reader = format_map[z]
-        else:
+        if z is None or z not in format_map.keys():
             logging.error(
                 "Could not determine format of annotation file. Please provide it explicitly."
             )
             sys.exit(1)
+        else:
+            annot_reader = format_map[z]
     else:
         fmt = params.format.lower()
-        if fmt not in ["gtf", "gff3"]:
+        if fmt not in format_map.keys():
             logging.error(
                 f'Format must be either "gtf" or "gff3", but {fmt} was provided.'
             )

From 66227f7069c072054297e078b600dcbbafa0f404 Mon Sep 17 00:00:00 2001
From: rob-p <rob.patro@gmail.com>
Date: Fri, 23 Jun 2023 16:35:45 -0400
Subject: [PATCH 2/4] make flake8 happy

---
 src/pyroe/id_to_name.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/pyroe/id_to_name.py b/src/pyroe/id_to_name.py
index 14c5ad1..caa36cf 100644
--- a/src/pyroe/id_to_name.py
+++ b/src/pyroe/id_to_name.py
@@ -19,7 +19,7 @@ def id_to_name(params):
         if len(suffs) >= 1:
             # look at the final suffix
             z = suffs[-1]
-            # if the final suffix is gz and there are 
+            # if the final suffix is gz and there are
             # suffixes preceding it, check the penultimate
             # one and use that
             if z == "gz" and len(suffs) > 1:

From fa4838858b2d52e44f995bd8e13067a8f5250850 Mon Sep 17 00:00:00 2001
From: rob-p <rob.patro@gmail.com>
Date: Fri, 23 Jun 2023 16:43:19 -0400
Subject: [PATCH 3/4] pin the versions of dependencies in github actions

---
 .github/workflows/testing.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 93402b4..1d7c65b 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -15,9 +15,9 @@ jobs:
         echo $CONDA/bin >> $GITHUB_PATH
     - name: Install dependencies
       run: |
-        conda install -n base python=3.9 conda-forge::biopython bioconda::pyranges packaging bioconda::scanpy pytest -y
+        conda install -n base python=3.9 conda-forge::biopython bioconda::numpy==1.23 bioconda::pyranges==0.0.120 packaging bioconda::scanpy pytest -y
 
     - name: pytest
       run: |
         pip install .
-        pytest
\ No newline at end of file
+        pytest

From 8d4bb650f80e4a86b1b40c7c3f21106571295b8d Mon Sep 17 00:00:00 2001
From: rob-p <rob.patro@gmail.com>
Date: Fri, 23 Jun 2023 16:49:22 -0400
Subject: [PATCH 4/4] pin the versions of dependencies in github actions

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 1d7c65b..8229600 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -15,7 +15,7 @@ jobs:
         echo $CONDA/bin >> $GITHUB_PATH
     - name: Install dependencies
       run: |
-        conda install -n base python=3.9 conda-forge::biopython bioconda::numpy==1.23 bioconda::pyranges==0.0.120 packaging bioconda::scanpy pytest -y
+        conda install -n base python=3.9 conda-forge::biopython numpy==1.23 bioconda::pyranges==0.0.120 packaging bioconda::scanpy pytest -y
 
     - name: pytest
       run: |