From 01eee9d331dd7338d3cc5572b7b0412bde80777c Mon Sep 17 00:00:00 2001
From: Anthony Tan <atan5133@gmail.com>
Date: Wed, 24 Apr 2024 15:05:11 -0700
Subject: [PATCH 01/10] update bedpe file format

---
 workflow/scripts/tools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflow/scripts/tools.py b/workflow/scripts/tools.py
index 5c1f7b7a0..7e591d884 100644
--- a/workflow/scripts/tools.py
+++ b/workflow/scripts/tools.py
@@ -46,7 +46,7 @@ def write_connections_bedpe_format(pred, outfile, score_column):
     towrite["chr2"] = pred["chr"]
     towrite["y1"] = pred["TargetGeneTSS"]
     towrite["y2"] = pred["TargetGeneTSS"]
-    towrite["name"] = pred["TargetGene"] + "_" + pred["name"]
+    towrite["name"] = pred["TargetGene"] + "|" + pred["name"]
     towrite["score"] = pred[score_column]
     towrite["strand1"] = "."
     towrite["strand2"] = "."

From 62dd7590dee8b73c27adf508a19c2d693bca936b Mon Sep 17 00:00:00 2001
From: Anthony Tan <atan5133@gmail.com>
Date: Tue, 30 Apr 2024 13:51:15 -0700
Subject: [PATCH 02/10] update bedpe file creation

---
 workflow/rules/predictions.smk |  2 +-
 workflow/scripts/tools.py      | 10 +++++++++-
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/workflow/rules/predictions.smk b/workflow/rules/predictions.smk
index 3829c3e32..5a68b499f 100644
--- a/workflow/rules/predictions.smk
+++ b/workflow/rules/predictions.smk
@@ -62,7 +62,7 @@ rule filter_predictions:
 		"../envs/abcenv.yml"
 	output:
 		enhPredictionsFull = os.path.join(RESULTS_DIR, "{biosample}", "Predictions", f"EnhancerPredictionsFull_{FILTERED_PREDICTION_FILE_FORMAT_TEMPLATE}.tsv"),
-		enhPredictionsFullBedpe = os.path.join(RESULTS_DIR, "{biosample}", "Predictions", f"EnhancerPredictionsFull_{FILTERED_PREDICTION_FILE_FORMAT_TEMPLATE}.bedpe"),
+		enhPredictionsFullBedpe = os.path.join(RESULTS_DIR, "{biosample}", "Predictions", f"EnhancerPredictionsFull_{FILTERED_PREDICTION_FILE_FORMAT_TEMPLATE}.bedpe.gz"),
 		enhPredictionsSlim = os.path.join(RESULTS_DIR, "{biosample}", "Predictions", f"EnhancerPredictions_{FILTERED_PREDICTION_FILE_FORMAT_TEMPLATE}.tsv"),
 		genePredictionsStats = os.path.join(RESULTS_DIR, "{biosample}", "Predictions", f"GenePredictionStats_{FILTERED_PREDICTION_FILE_FORMAT_TEMPLATE}.tsv")
 	resources:
diff --git a/workflow/scripts/tools.py b/workflow/scripts/tools.py
index 7e591d884..7b5621474 100644
--- a/workflow/scripts/tools.py
+++ b/workflow/scripts/tools.py
@@ -46,7 +46,15 @@ def write_connections_bedpe_format(pred, outfile, score_column):
     towrite["chr2"] = pred["chr"]
     towrite["y1"] = pred["TargetGeneTSS"]
     towrite["y2"] = pred["TargetGeneTSS"]
-    towrite["name"] = pred["TargetGene"] + "|" + pred["name"]
+    towrite["name"] = (
+        pred["TargetGene"]
+        + "|"
+        + pred["chr"]
+        + ":"
+        + pred["start"].astype(str)
+        + "-"
+        + pred["end"].astype(str)
+    )
     towrite["score"] = pred[score_column]
     towrite["strand1"] = "."
     towrite["strand2"] = "."

From 0e814de43f1dd199c507e0bc3d89ac9ad3cfe586 Mon Sep 17 00:00:00 2001
From: Anthony Tan <atan5133@gmail.com>
Date: Thu, 2 May 2024 11:55:29 -0700
Subject: [PATCH 03/10] clean up hic processing code

---
 workflow/scripts/predictor.py | 60 +++++++++++++++++------------------
 1 file changed, 30 insertions(+), 30 deletions(-)

diff --git a/workflow/scripts/predictor.py b/workflow/scripts/predictor.py
index 35bdda033..e3cf51934 100644
--- a/workflow/scripts/predictor.py
+++ b/workflow/scripts/predictor.py
@@ -103,29 +103,17 @@ def make_pred_table(chromosome, enh, genes, window, chrom_sizes_map: Dict[str, i
     return pred
 
 
-def create_df_from_records(records, hic_resolution):
+def fill_diagonals(df, hic_resolution):
     """
-    The bins returned from hic straw are in hic_resolution increments
-    If resolution = 5k, we want to normalize the bins such that:
-        5000 -> bin 1
-        10000 -> bin 2
-        ...
-        100k -> bin 20
-    Where the left number is the genomic position of the bin
-
-    We also record the neighboring bins of the diagonals, as we
-    want to replace the value with the neighbors later
+    Fill diagonals based on the neighbors
+    We want to search neighboring bins
+    If hic_resolution is < 5kb, make sure we use a search space of 5kb for our
+    neighbors
     """
-    df = pd.DataFrame(records, columns=["binX", "binY", "counts"])
-    df["binX"] = np.floor(df["binX"] / hic_resolution).astype(int)
-    df["binY"] = np.floor(df["binY"] / hic_resolution).astype(int)
-    df = df.set_index(["binX", "binY"])  # Set indexes for performance
     diagonal_bins = df[
         df.index.get_level_values("binX") == df.index.get_level_values("binY")
     ]
-    # Provide max neighbor counts
-    # We'll divide by the normalizing constant later when replacing the value
-    for (binX, binY), _ in diagonal_bins.iterrows():
+    for (binX, binX), _ in diagonal_bins.iterrows():
         left_bin_count, right_bin_count = 0, 0
         left_binX = binX - 1
         left_binY = binX
@@ -137,9 +125,26 @@ def create_df_from_records(records, hic_resolution):
         if (right_binX, right_binY) in df.index:
             right_bin_count = df.loc[(right_binX, right_binY), "counts"]
 
-        df.loc[(binX, binY), "max_neighbor_count"] = max(
-            left_bin_count, right_bin_count
-        )
+        df.loc[(binX, binX), "counts"] = max(left_bin_count, right_bin_count)
+
+
+def create_df_from_records(records, hic_resolution):
+    """
+    The bins returned from hic straw are in hic_resolution increments
+    If resolution = 5k, we want to normalize the bins such that:
+        5000 -> bin 1
+        10000 -> bin 2
+        ...
+        100k -> bin 20
+    Where the left number is the genomic position of the bin
+
+    We also handle filling the diagonals differently
+    """
+    df = pd.DataFrame(records, columns=["binX", "binY", "counts"])
+    df["binX"] = np.floor(df["binX"] / hic_resolution).astype(int)
+    df["binY"] = np.floor(df["binY"] / hic_resolution).astype(int)
+    df = df.set_index(["binX", "binY"])  # Set indexes for performance
+    fill_diagonals(df, hic_resolution)
     return df
 
 
@@ -234,20 +239,15 @@ def add_hic_from_hic_file(pred, hic_file, chromosome, hic_resolution):
                 suffixes=(None, "_"),
             )
             if "counts_" in pred:
+                # After the first join, we have to merge the new records into
+                # the existing count column. It's really just replacing the
+                # nan values in pred_df with new values from latest records
                 pred["counts"] = np.max(pred[["counts", "counts_"]], axis=1)
                 pred.drop("counts_", inplace=True, axis=1)
 
-                pred["max_neighbor_count"] = np.max(
-                    pred[["max_neighbor_count", "max_neighbor_count_"]], axis=1
-                )
-                pred.drop("max_neighbor_count_", inplace=True, axis=1)
-
     row_mean = np.mean(list(bin_sums.values()))
     # normalize hic_contact by the row_mean to reflect a doubly stochastic hic matrix
     pred["counts"] /= row_mean
-    pred["max_neighbor_count"] /= row_mean
-    # Fill in diagonals with the max of neighbors
-    pred["counts"] = pred["max_neighbor_count"].combine_first(pred["counts"])
 
     pred.drop(
         [
@@ -463,7 +463,7 @@ def add_hic_pseudocount(pred, args):
         args.hic_pseudocount_distance,
         args.hic_gamma,
         args.hic_scale,
-        args.hic_resolution,
+        args.hic_pseudocount_distance,
     )
     pred["hic_pseudocount"] = pd.DataFrame(
         {"a": pred["powerlaw_contact"], "b": pseudocount_distance}

From dc1dde7bea1f8387385ede924e91c975c11b87c4 Mon Sep 17 00:00:00 2001
From: Anthony Tan <atan5133@gmail.com>
Date: Thu, 2 May 2024 12:20:15 -0700
Subject: [PATCH 04/10] support adaptable search space for hic

---
 workflow/scripts/predictor.py | 23 +++++++++++------------
 1 file changed, 11 insertions(+), 12 deletions(-)

diff --git a/workflow/scripts/predictor.py b/workflow/scripts/predictor.py
index e3cf51934..f3e7b147f 100644
--- a/workflow/scripts/predictor.py
+++ b/workflow/scripts/predictor.py
@@ -113,19 +113,18 @@ def fill_diagonals(df, hic_resolution):
     diagonal_bins = df[
         df.index.get_level_values("binX") == df.index.get_level_values("binY")
     ]
+    search_space_bins = 1
+    if hic_resolution < 5000:
+        search_space_bins = math.ceil(5000 / hic_resolution)
     for (binX, binX), _ in diagonal_bins.iterrows():
-        left_bin_count, right_bin_count = 0, 0
-        left_binX = binX - 1
-        left_binY = binX
-        if (left_binX, left_binY) in df.index:
-            left_bin_count = df.loc[(left_binX, left_binY), "counts"]
-
-        right_binX = binX
-        right_binY = binX + 1
-        if (right_binX, right_binY) in df.index:
-            right_bin_count = df.loc[(right_binX, right_binY), "counts"]
-
-        df.loc[(binX, binX), "counts"] = max(left_bin_count, right_bin_count)
+        max_contact = 0
+        for i in range(1, search_space_bins+1):
+            left_bin = (binX - i, binX)
+            right_bin = (binX, binX + i)  # we have to look above b/c we haven't processed right bin yet
+            for bin in [left_bin, right_bin]:
+                if bin in df.index:
+                    max_contact = max(max_contact, df.loc[bin, "counts"])
+        df.loc[(binX, binX), "counts"] = max_contact
 
 
 def create_df_from_records(records, hic_resolution):

From 22d243e677099d36cf4632f67f7714c49425a226 Mon Sep 17 00:00:00 2001
From: Anthony Tan <atan5133@gmail.com>
Date: Fri, 3 May 2024 14:54:45 -0700
Subject: [PATCH 05/10] only support 5kb res for hic

---
 docs/usage/getting_started.rst | 2 +-
 workflow/rules/utils.smk       | 2 ++
 workflow/scripts/predictor.py  | 7 +++++--
 3 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/docs/usage/getting_started.rst b/docs/usage/getting_started.rst
index b69cc9382..f2709f210 100644
--- a/docs/usage/getting_started.rst
+++ b/docs/usage/getting_started.rst
@@ -123,7 +123,7 @@ biosamples config is a tsv separated file with the following columns
 	- If you dumped hic into a directory via JuicerTools, use ``juicebox``
 	- If you have a bedpe file for contact, it should be a tab delimited file containing 8 columns (chr1,start1,end1,chr2,start2,end2,name,score)
 #. HiC_resolution (int)
-	- Recommended to use 5KB (kilobases)
+	- Currently only 5KB (kilobases) is supported
 	- 5KB means dna regions are bucketed into 5KB bins and we measure contact between those bins
 #. alt_TSS (optional; not recommended to fill)
 	- Alternative TSS reference file 
diff --git a/workflow/rules/utils.smk b/workflow/rules/utils.smk
index f24022de5..0dadc9119 100644
--- a/workflow/rules/utils.smk
+++ b/workflow/rules/utils.smk
@@ -106,6 +106,8 @@ def _validate_hic_info(row: pd.Series):
 	if row["HiC_file"]:
 		if not (row["HiC_type"] and row["HiC_resolution"]):
 			raise InvalidConfig("Must provide HiC type and resolution with file")
+		if row["HiC_resolution"] != 5000:
+			raise InvalidConfig("Only 5kb resolution supported at the moment")
 
 def _validate_biosamples_config(biosamples_config):
 	"""
diff --git a/workflow/scripts/predictor.py b/workflow/scripts/predictor.py
index f3e7b147f..f5d21f558 100644
--- a/workflow/scripts/predictor.py
+++ b/workflow/scripts/predictor.py
@@ -118,9 +118,12 @@ def fill_diagonals(df, hic_resolution):
         search_space_bins = math.ceil(5000 / hic_resolution)
     for (binX, binX), _ in diagonal_bins.iterrows():
         max_contact = 0
-        for i in range(1, search_space_bins+1):
+        for i in range(1, search_space_bins + 1):
             left_bin = (binX - i, binX)
-            right_bin = (binX, binX + i)  # we have to look above b/c we haven't processed right bin yet
+            right_bin = (
+                binX,
+                binX + i,
+            )  # we have to look above b/c we haven't processed right bin yet
             for bin in [left_bin, right_bin]:
                 if bin in df.index:
                     max_contact = max(max_contact, df.loc[bin, "counts"])

From 93f8533410693caf6df9c4675e35661676010ee9 Mon Sep 17 00:00:00 2001
From: Anthony Tan <10254642+atancoder@users.noreply.github.com>
Date: Mon, 6 May 2024 16:56:02 -0700
Subject: [PATCH 06/10] Update getting_started.rst

---
 docs/usage/getting_started.rst | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/usage/getting_started.rst b/docs/usage/getting_started.rst
index b69cc9382..10bc7be2c 100644
--- a/docs/usage/getting_started.rst
+++ b/docs/usage/getting_started.rst
@@ -15,6 +15,7 @@ Installation
 	- Make sure you're not using strict channel priorities: ``conda config --set channel_priority flexible``. Otherwise, you may encounter package conflicts later when installing abc. 
 	- To install mamba: ``conda create -n mamba -c conda-forge mamba -y``
 		- We recommend mamba as using conda can take 1hr+ for setup
+		- See troubleshooting page if you run into issues
 
 
 Setup Conda Environment

From d2cca0339ff711740e3c3c849a328939a6f44c50 Mon Sep 17 00:00:00 2001
From: Anthony Tan <atan5133@gmail.com>
Date: Thu, 9 May 2024 12:14:54 -0700
Subject: [PATCH 07/10] remove default for hic_psuedocount_distance in
 predict.py since it's confusing with default in the config

---
 workflow/scripts/predict.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflow/scripts/predict.py b/workflow/scripts/predict.py
index 05d5e8944..6d5f9aef6 100644
--- a/workflow/scripts/predict.py
+++ b/workflow/scripts/predict.py
@@ -55,7 +55,7 @@ class formatter(
     parser.add_argument(
         "--hic_pseudocount_distance",
         type=int,
-        default=1e6,
+        required=True,
         help="A pseudocount is added equal to the powerlaw fit at this distance",
     )
     parser.add_argument(

From f3b9bffd185d31a2eb4aee6a60587648de32b616 Mon Sep 17 00:00:00 2001
From: Anthony Tan <atan5133@gmail.com>
Date: Wed, 29 May 2024 14:01:07 -0700
Subject: [PATCH 08/10] utilize amazon link as the encode link leads to a
 segfault in CircleCI

---
 tests/config/test_biosamples.tsv | 2 +-
 tests/test_predictor.py          | 2 +-
 workflow/envs/abcenv.yml         | 3 ++-
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/tests/config/test_biosamples.tsv b/tests/config/test_biosamples.tsv
index 3025d423c..dc5fda28a 100644
--- a/tests/config/test_biosamples.tsv
+++ b/tests/config/test_biosamples.tsv
@@ -1,3 +1,3 @@
 biosample	DHS	ATAC	H3K27ac	default_accessibility_feature	HiC_file	HiC_type	HiC_resolution	alt_TSS	alt_genes
-K562_chr22	example_chr/chr22/ENCFF860XAE.chr22.sorted.se.bam		example_chr/chr22/ENCFF790GFL.chr22.sorted.se.bam	DHS	https://www.encodeproject.org/files/ENCFF621AIY/@@download/ENCFF621AIY.hic	hic	5000	example_chr/chr22/RefSeqCurated.170308.bed.CollapsedGeneBounds.chr22.hg38.TSS500bp.bed	example_chr/chr22/RefSeqCurated.170308.bed.CollapsedGeneBounds.chr22.hg38.bed
+K562_chr22	example_chr/chr22/ENCFF860XAE.chr22.sorted.se.bam		example_chr/chr22/ENCFF790GFL.chr22.sorted.se.bam	DHS	https://encode-public.s3.amazonaws.com/2022/05/15/0571c671-3645-4f92-beae-51dfd3f42c36/ENCFF621AIY.hic	hic	5000	example_chr/chr22/RefSeqCurated.170308.bed.CollapsedGeneBounds.chr22.hg38.TSS500bp.bed	example_chr/chr22/RefSeqCurated.170308.bed.CollapsedGeneBounds.chr22.hg38.bed
 K562_chr22_tagAlign		example_chr/chr22/chr22.sorted.tagAlign.gz		ATAC				example_chr/chr22/RefSeqCurated.170308.bed.CollapsedGeneBounds.chr22.hg38.TSS500bp.bed	example_chr/chr22/RefSeqCurated.170308.bed.CollapsedGeneBounds.chr22.hg38.bed
diff --git a/tests/test_predictor.py b/tests/test_predictor.py
index cbfb998ed..ad9afcf11 100644
--- a/tests/test_predictor.py
+++ b/tests/test_predictor.py
@@ -7,7 +7,7 @@
 from predictor import add_hic_from_hic_file
 import pandas as pd
 
-HIC_FILE = "https://www.encodeproject.org/files/ENCFF621AIY/@@download/ENCFF621AIY.hic"
+HIC_FILE = "https://encode-public.s3.amazonaws.com/2022/05/15/0571c671-3645-4f92-beae-51dfd3f42c36/ENCFF621AIY.hic"
 
 # this file has 3k rows of E-G pairs with valid contact values
 # contact values were generated from the original doubly stochastic method
diff --git a/workflow/envs/abcenv.yml b/workflow/envs/abcenv.yml
index f526f5ea2..dd3e63b86 100644
--- a/workflow/envs/abcenv.yml
+++ b/workflow/envs/abcenv.yml
@@ -13,6 +13,7 @@ dependencies:
   - numpy
   - pandas
   - pybigwig
+  - pulp<2.8 # Pin pulp <2.8 for snakemake: https://github.com/snakemake/snakemake/issues/2607
   - pip
   - pyarrow
   - pyranges
@@ -35,4 +36,4 @@ dependencies:
   - zlib
   - pip:
     - sphinx_rtd_theme
-    - hic-straw
\ No newline at end of file
+    - hic-straw

From 6ddc6ceba3e439a5ee1ca29681539e33b2476dcc Mon Sep 17 00:00:00 2001
From: Anthony Tan <atan5133@gmail.com>
Date: Thu, 30 May 2024 11:12:04 -0700
Subject: [PATCH 09/10] update release conda env

---
 workflow/envs/release.yml | 356 ++++++++++++++++++--------------------
 1 file changed, 165 insertions(+), 191 deletions(-)

diff --git a/workflow/envs/release.yml b/workflow/envs/release.yml
index 959a66c22..64383552b 100644
--- a/workflow/envs/release.yml
+++ b/workflow/envs/release.yml
@@ -9,44 +9,42 @@ dependencies:
   - _openmp_mutex=4.5=2_gnu
   - _r-mutex=1.0.1=anacondar_1
   - aioeasywebdav=2.4.0=pyha770c72_0
-  - aiohttp=3.9.3=py310h2372a71_0
+  - aiohttp=3.9.5=py310h2372a71_0
   - aiosignal=1.3.1=pyhd8ed1ab_0
   - alabaster=0.7.16=pyhd8ed1ab_0
   - alsa-lib=1.2.11=hd590300_1
   - amply=0.1.6=pyhd8ed1ab_0
   - appdirs=1.4.4=pyh9f0ad1d_0
-  - archspec=0.2.3=pyhd8ed1ab_0
   - async-timeout=4.0.3=pyhd8ed1ab_0
   - attmap=0.13.2=pyhd8ed1ab_0
   - attr=2.5.1=h166bdaf_1
   - attrs=23.2.0=pyh71513ae_0
-  - aws-c-auth=0.7.16=h79b3bcb_6
-  - aws-c-cal=0.6.10=hb29e0c7_1
-  - aws-c-common=0.9.13=hd590300_0
-  - aws-c-compression=0.2.18=hecc5fa9_1
-  - aws-c-event-stream=0.4.2=hf9b2f7b_4
-  - aws-c-http=0.8.1=h5d7533a_5
-  - aws-c-io=0.14.5=h50678d4_1
-  - aws-c-mqtt=0.10.2=hf479d2b_4
-  - aws-c-s3=0.5.2=h4ad9680_0
-  - aws-c-sdkutils=0.1.15=hecc5fa9_1
-  - aws-checksums=0.1.18=hecc5fa9_1
-  - aws-crt-cpp=0.26.2=h19f5d62_7
-  - aws-sdk-cpp=1.11.267=h5606698_1
+  - aws-c-auth=0.7.22=h96bc93b_2
+  - aws-c-cal=0.6.14=h88a6e22_1
+  - aws-c-common=0.9.19=h4ab18f5_0
+  - aws-c-compression=0.2.18=h83b837d_6
+  - aws-c-event-stream=0.4.2=ha47c788_12
+  - aws-c-http=0.8.1=h29d6fba_17
+  - aws-c-io=0.14.8=h21d4f22_5
+  - aws-c-mqtt=0.10.4=h759edc4_4
+  - aws-c-s3=0.5.9=h594631b_3
+  - aws-c-sdkutils=0.1.16=h83b837d_2
+  - aws-checksums=0.1.18=h83b837d_6
+  - aws-crt-cpp=0.26.9=he3a8b3b_0
+  - aws-sdk-cpp=1.11.329=hba8bd5f_3
   - babel=2.14.0=pyhd8ed1ab_0
-  - bcrypt=4.1.2=py310hcb5633a_0
+  - bcrypt=4.1.3=py310he421c4c_0
   - bedtools=2.26.0=0
-  - binutils_impl_linux-64=2.40=hf600244_0
-  - black=24.2.0=py310hff52083_0
-  - boltons=23.1.1=pyhd8ed1ab_0
-  - boto3=1.34.55=pyhd8ed1ab_0
-  - botocore=1.34.56=pyge310_1234567_0
+  - binutils_impl_linux-64=2.40=ha1999f0_1
+  - black=24.4.2=py310hff52083_0
+  - boto3=1.34.114=pyhd8ed1ab_0
+  - botocore=1.34.114=pyge310_1234567_0
   - brotli=1.1.0=hd590300_1
   - brotli-bin=1.1.0=hd590300_1
   - brotli-python=1.1.0=py310hc6cd4ac_1
   - bwidget=1.9.14=ha770c72_1
   - bzip2=1.0.8=hd590300_5
-  - c-ares=1.27.0=hd590300_0
+  - c-ares=1.28.1=hd590300_0
   - ca-certificates=2024.2.2=hbcca054_0
   - cachetools=5.3.3=pyhd8ed1ab_0
   - cairo=1.18.0=h3faef2a_0
@@ -57,277 +55,257 @@ dependencies:
   - coin-or-cbc=2.10.10=h9002f0b_0
   - coin-or-cgl=0.60.7=h516709c_0
   - coin-or-clp=1.17.8=h1ee7a9c_0
-  - coin-or-osi=0.108.8=ha2443b9_0
-  - coin-or-utils=2.11.9=hee58242_0
+  - coin-or-osi=0.108.10=haf5fa05_0
+  - coin-or-utils=2.11.11=hee58242_0
   - coincbc=2.10.10=0_metapackage
   - colorama=0.4.6=pyhd8ed1ab_0
-  - conda=24.1.2=py310hff52083_0
-  - conda-libmamba-solver=24.1.0=pyhd8ed1ab_0
-  - conda-package-handling=2.2.0=pyh38be061_0
-  - conda-package-streaming=0.9.0=pyhd8ed1ab_0
   - configargparse=1.7=pyhd8ed1ab_0
   - connection_pool=0.0.3=pyhd3deb0d_0
-  - contourpy=1.2.0=py310hd41b1e2_0
-  - cryptography=42.0.5=py310h75e40e8_0
-  - curl=8.5.0=hca28451_0
+  - contourpy=1.2.1=py310hd41b1e2_0
+  - cryptography=42.0.7=py310hb1bd9d3_0
+  - curl=8.8.0=he654da7_0
   - cycler=0.12.1=pyhd8ed1ab_0
   - datrie=0.8.2=py310h2372a71_7
   - dbus=1.13.6=h5008d03_3
   - defusedxml=0.7.1=pyhd8ed1ab_0
-  - distro=1.9.0=pyhd8ed1ab_0
-  - docutils=0.20.1=py310hff52083_3
   - dpath=2.1.6=pyha770c72_0
   - dropbox=11.36.2=pyhd8ed1ab_0
   - eido=0.2.2=pyhd8ed1ab_0
   - exceptiongroup=1.2.0=pyhd8ed1ab_2
-  - execnet=2.0.2=pyhd8ed1ab_0
-  - expat=2.5.0=hcb278e6_1
+  - execnet=2.1.1=pyhd8ed1ab_0
+  - expat=2.6.2=h59595ed_0
   - filechunkio=1.8=py_2
-  - fmt=10.2.1=h00ab1b0_0
   - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
   - font-ttf-inconsolata=3.000=h77eed37_0
   - font-ttf-source-code-pro=2.038=h77eed37_0
-  - font-ttf-ubuntu=0.83=h77eed37_1
+  - font-ttf-ubuntu=0.83=h77eed37_2
   - fontconfig=2.14.2=h14ed4e7_0
   - fonts-conda-ecosystem=1=0
   - fonts-conda-forge=1=0
-  - fonttools=4.49.0=py310h2372a71_0
+  - fonttools=4.52.4=py310hc51659f_0
   - freetype=2.12.1=h267a509_2
   - fribidi=1.0.10=h36c2ea0_0
   - frozenlist=1.4.1=py310h2372a71_0
   - ftputil=5.1.0=pyhd8ed1ab_0
-  - gcc=13.2.0=h574f8da_2
-  - gcc_impl_linux-64=13.2.0=h338b0a0_5
-  - gettext=0.21.1=h27087fc_0
+  - gcc=13.2.0=hc7bed06_7
+  - gcc_impl_linux-64=13.2.0=h9eb54c0_7
+  - gettext=0.22.5=h59595ed_2
+  - gettext-tools=0.22.5=h59595ed_2
   - gflags=2.2.2=he1b5a44_1004
-  - gfortran_impl_linux-64=13.2.0=h76e1118_5
+  - gfortran_impl_linux-64=13.2.0=h738fc78_7
   - gitdb=4.0.11=pyhd8ed1ab_0
-  - gitpython=3.1.42=pyhd8ed1ab_0
-  - glib=2.78.1=hfc55251_0
-  - glib-tools=2.78.1=hfc55251_0
+  - gitpython=3.1.43=pyhd8ed1ab_0
+  - glib=2.80.2=hf974151_0
+  - glib-tools=2.80.2=hb6ce0ca_0
   - glog=0.7.0=hed5481d_0
-  - google-api-core=2.17.1=pyhd8ed1ab_0
-  - google-api-python-client=2.121.0=pyhd8ed1ab_0
-  - google-auth=2.28.1=pyhca7485f_0
+  - google-api-core=2.19.0=pyhd8ed1ab_0
+  - google-api-python-client=2.131.0=pyhd8ed1ab_0
+  - google-auth=2.29.0=pyhca7485f_0
   - google-auth-httplib2=0.2.0=pyhd8ed1ab_0
   - google-cloud-core=2.4.1=pyhd8ed1ab_0
-  - google-cloud-storage=2.14.0=pyhca7485f_0
+  - google-cloud-storage=2.16.0=pyhca7485f_0
   - google-crc32c=1.1.2=py310hc5c09a0_5
   - google-resumable-media=2.7.0=pyhd8ed1ab_0
-  - googleapis-common-protos=1.62.0=pyhd8ed1ab_0
-  - graphite2=1.3.13=h58526e2_1001
-  - grpcio=1.61.1=py310h1b8f574_1
-  - gst-plugins-base=1.22.7=h8e1006c_0
-  - gstreamer=1.22.7=h98fc4e7_0
-  - gxx=13.2.0=h574f8da_2
-  - gxx_impl_linux-64=13.2.0=h338b0a0_5
-  - harfbuzz=8.3.0=h3d44ed6_0
-  - htslib=1.19.1=h81da01d_2
+  - googleapis-common-protos=1.63.0=pyhd8ed1ab_0
+  - graphite2=1.3.13=h59595ed_1003
+  - grpcio=1.62.2=py310h1b8f574_0
+  - gst-plugins-base=1.24.4=h9ad1361_0
+  - gstreamer=1.24.4=haf2f30d_0
+  - gxx=13.2.0=hc7bed06_7
+  - gxx_impl_linux-64=13.2.0=h2a599c4_7
+  - harfbuzz=8.5.0=hfac3d4d_0
+  - htslib=1.20=h81da01d_0
   - httplib2=0.22.0=pyhd8ed1ab_0
   - humanfriendly=10.0=pyhd8ed1ab_6
   - icu=73.2=h59595ed_0
-  - idna=3.6=pyhd8ed1ab_0
+  - idna=3.7=pyhd8ed1ab_0
   - imagesize=1.4.1=pyhd8ed1ab_0
-  - importlib-metadata=7.0.1=pyha770c72_0
-  - importlib_resources=6.1.2=pyhd8ed1ab_0
+  - importlib-metadata=7.1.0=pyha770c72_0
+  - importlib_resources=6.4.0=pyhd8ed1ab_0
   - iniconfig=2.0.0=pyhd8ed1ab_0
-  - jinja2=3.1.3=pyhd8ed1ab_0
+  - jinja2=3.1.4=pyhd8ed1ab_0
   - jmespath=1.0.1=pyhd8ed1ab_0
-  - jsonpatch=1.33=pyhd8ed1ab_0
-  - jsonpointer=2.4=py310hff52083_3
-  - jsonschema=4.21.1=pyhd8ed1ab_0
+  - jsonschema=4.22.0=pyhd8ed1ab_0
   - jsonschema-specifications=2023.12.1=pyhd8ed1ab_0
-  - jupyter_core=5.7.1=py310hff52083_0
+  - jupyter_core=5.7.2=py310hff52083_0
   - kernel-headers_linux-64=2.6.32=he073ed8_17
   - keyutils=1.6.1=h166bdaf_0
   - kiwisolver=1.4.5=py310hd41b1e2_1
   - krb5=1.21.2=h659d440_0
   - lame=3.100=h166bdaf_1003
-  - lcms2=2.15=h7f713cb_2
-  - ld_impl_linux-64=2.40=h41732ed_0
+  - lcms2=2.16=hb7c19ff_0
+  - ld_impl_linux-64=2.40=hf3520f5_1
   - lerc=4.0.0=h27087fc_0
-  - libabseil=20240116.1=cxx17_h59595ed_2
-  - libarchive=3.7.2=h2aa1ff5_1
-  - libarrow=15.0.0=h5001e6d_7_cpu
-  - libarrow-acero=15.0.0=h59595ed_7_cpu
-  - libarrow-dataset=15.0.0=h59595ed_7_cpu
-  - libarrow-flight=15.0.0=hf334d8d_7_cpu
-  - libarrow-flight-sql=15.0.0=h469e5c9_7_cpu
-  - libarrow-gandiva=15.0.0=h3f306ff_7_cpu
-  - libarrow-substrait=15.0.0=h469e5c9_7_cpu
-  - libblas=3.9.0=21_linux64_openblas
+  - libabseil=20240116.2=cxx17_h59595ed_0
+  - libarrow=16.1.0=hcb6531f_6_cpu
+  - libarrow-acero=16.1.0=hac33072_6_cpu
+  - libarrow-dataset=16.1.0=hac33072_6_cpu
+  - libarrow-substrait=16.1.0=h7e0c224_6_cpu
+  - libasprintf=0.22.5=h661eb56_2
+  - libasprintf-devel=0.22.5=h661eb56_2
+  - libblas=3.9.0=22_linux64_openblas
   - libbrotlicommon=1.1.0=hd590300_1
   - libbrotlidec=1.1.0=hd590300_1
   - libbrotlienc=1.1.0=hd590300_1
   - libcap=2.69=h0f662aa_0
-  - libcblas=3.9.0=21_linux64_openblas
-  - libclang=15.0.7=default_hb11cfb5_4
-  - libclang13=15.0.7=default_ha2b6cf4_4
+  - libcblas=3.9.0=22_linux64_openblas
+  - libclang-cpp15=15.0.7=default_h127d8a8_5
+  - libclang13=18.1.6=default_h5d6823c_0
   - libcrc32c=1.1.2=h9c3ff4c_0
   - libcups=2.3.3=h4637d8d_4
-  - libcurl=8.5.0=hca28451_0
-  - libdeflate=1.18=h0b41bf4_0
+  - libcurl=8.8.0=hca28451_0
+  - libdeflate=1.20=hd590300_0
   - libedit=3.1.20191231=he28a2e2_2
   - libev=4.33=hd590300_2
   - libevent=2.1.12=hf998b51_1
-  - libexpat=2.5.0=hcb278e6_1
+  - libexpat=2.6.2=h59595ed_0
   - libffi=3.4.2=h7f98852_5
   - libflac=1.4.3=h59595ed_0
   - libgcc=7.2.0=h69d50b8_2
-  - libgcc-devel_linux-64=13.2.0=ha9c7c90_105
-  - libgcc-ng=13.2.0=h807b86a_5
+  - libgcc-devel_linux-64=13.2.0=hceb6213_107
+  - libgcc-ng=13.2.0=h77fa898_7
   - libgcrypt=1.10.3=hd590300_0
-  - libgfortran-ng=13.2.0=h69a702a_5
-  - libgfortran5=13.2.0=ha4646dd_5
-  - libglib=2.78.1=hebfc3b9_0
-  - libgomp=13.2.0=h807b86a_5
-  - libgoogle-cloud=2.21.0=h72bcb37_2
-  - libgoogle-cloud-storage=2.21.0=hc7a4891_2
-  - libgpg-error=1.48=h71f35ed_0
-  - libgrpc=1.61.1=h42401df_1
+  - libgettextpo=0.22.5=h59595ed_2
+  - libgettextpo-devel=0.22.5=h59595ed_2
+  - libgfortran-ng=13.2.0=h69a702a_7
+  - libgfortran5=13.2.0=hca663fb_7
+  - libglib=2.80.2=hf974151_0
+  - libgomp=13.2.0=h77fa898_7
+  - libgoogle-cloud=2.24.0=h2736e30_0
+  - libgoogle-cloud-storage=2.24.0=h3d9a0c8_0
+  - libgpg-error=1.49=h4f305b6_0
+  - libgrpc=1.62.2=h15f2491_0
   - libiconv=1.17=hd590300_2
-  - libjpeg-turbo=2.1.5.1=hd590300_1
-  - liblapack=3.9.0=21_linux64_openblas
-  - liblapacke=3.9.0=21_linux64_openblas
+  - libjpeg-turbo=3.0.0=hd590300_1
+  - liblapack=3.9.0=22_linux64_openblas
+  - liblapacke=3.9.0=22_linux64_openblas
   - libllvm15=15.0.7=hb3ce162_4
-  - libllvm16=16.0.6=hb3ce162_3
-  - libmamba=1.5.7=had39da4_0
-  - libmambapy=1.5.7=py310h39ff949_0
+  - libllvm18=18.1.6=hb77312f_0
   - libnghttp2=1.58.0=h47da74e_1
-  - libnl=3.9.0=hd590300_0
   - libnsl=2.0.1=hd590300_0
-  - libnuma=2.0.16=h0b41bf4_1
   - libogg=1.3.4=h7f98852_1
-  - libopenblas=0.3.26=pthreads_h413a1c8_0
+  - libopenblas=0.3.27=pthreads_h413a1c8_0
   - libopus=1.3.1=h7f98852_1
-  - libparquet=15.0.0=h352af49_7_cpu
+  - libparquet=16.1.0=h6a7eafb_6_cpu
   - libpng=1.6.43=h2797004_0
-  - libpq=15.6=h088ca5b_0
-  - libprotobuf=4.25.2=h08a7969_1
+  - libpq=16.3=ha72fbe1_0
+  - libprotobuf=4.25.3=h08a7969_0
   - libre2-11=2023.09.01=h5a48ba9_2
-  - libsanitizer=13.2.0=h7e041cc_5
+  - libsanitizer=13.2.0=h6ddb7a1_7
   - libsndfile=1.2.2=hc60ed4a_1
   - libsodium=1.0.18=h36c2ea0_1
-  - libsolv=0.7.28=hfc55251_0
-  - libsqlite=3.45.1=h2797004_0
+  - libsqlite=3.45.3=h2797004_0
   - libssh2=1.11.0=h0841786_0
-  - libstdcxx-devel_linux-64=13.2.0=ha9c7c90_105
-  - libstdcxx-ng=13.2.0=h7e041cc_5
+  - libstdcxx-devel_linux-64=13.2.0=hceb6213_107
+  - libstdcxx-ng=13.2.0=hc0a3c3a_7
   - libsystemd0=255=h3516f8a_1
   - libthrift=0.19.0=hb90f79a_1
-  - libtiff=4.6.0=h8b53f26_0
+  - libtiff=4.6.0=h1dd3fc0_3
   - libutf8proc=2.8.0=h166bdaf_0
   - libuuid=2.38.1=h0b41bf4_0
   - libvorbis=1.3.7=h9c3ff4c_0
-  - libwebp-base=1.3.2=hd590300_0
+  - libwebp-base=1.4.0=hd590300_0
   - libxcb=1.15=h0b41bf4_0
   - libxcrypt=4.4.36=hd590300_1
-  - libxkbcommon=1.6.0=hd429924_1
-  - libxml2=2.12.5=h232c23b_0
-  - libzlib=1.2.13=hd590300_5
+  - libxkbcommon=1.7.0=h662e7e4_0
+  - libxml2=2.12.7=hc051c1a_0
+  - libzlib=1.2.13=h4ab18f5_6
   - logmuse=0.2.6=pyh8c360ce_0
   - lz4-c=1.9.4=hcb278e6_0
-  - lzo=2.10=h516909a_1000
   - macs2=2.2.9.1=py310h4b81fae_0
   - make=4.3=hd18ef5c_1
   - markdown-it-py=3.0.0=pyhd8ed1ab_0
   - markupsafe=2.1.5=py310h2372a71_0
-  - matplotlib=3.8.3=py310hff52083_0
-  - matplotlib-base=3.8.3=py310h62c0568_0
+  - matplotlib=3.8.4=py310hff52083_2
+  - matplotlib-base=3.8.4=py310hef631a5_2
   - mdurl=0.1.2=pyhd8ed1ab_0
-  - menuinst=2.0.2=py310hff52083_0
-  - mpg123=1.32.4=h59595ed_0
+  - mpg123=1.32.6=h59595ed_0
   - multidict=6.0.5=py310h2372a71_0
   - munkres=1.0.7=py_1
   - mypy_extensions=1.0.0=pyha770c72_0
-  - mysql-common=8.0.33=hf1915f5_6
-  - mysql-libs=8.0.33=hca2cd23_6
+  - mysql-common=8.3.0=hf1915f5_4
+  - mysql-libs=8.3.0=hca2cd23_4
   - natsort=8.4.0=pyhd8ed1ab_0
-  - nbformat=5.9.2=pyhd8ed1ab_0
-  - ncls=0.0.68=py310h4b81fae_1
-  - ncurses=6.4=h59595ed_2
+  - nbformat=5.10.4=pyhd8ed1ab_0
+  - ncls=0.0.68=py310h4b81fae_2
+  - ncurses=6.5=h59595ed_0
   - nspr=4.35=h27087fc_0
-  - nss=3.98=h1d7d5a4_0
+  - nss=3.100=hca3bf56_0
   - numpy=1.26.4=py310hb13e2d6_0
   - oauth2client=4.1.3=py_0
   - openjpeg=2.5.2=h488ebb8_0
-  - openssl=3.2.1=hd590300_0
-  - orc=1.9.2=h00e871a_2
-  - packaging=23.2=pyhd8ed1ab_0
-  - pandas=2.2.1=py310hcc13569_0
-  - pango=1.50.14=ha41ecd1_2
+  - openssl=3.3.0=h4ab18f5_3
+  - orc=2.0.1=h17fec99_1
+  - packaging=24.0=pyhd8ed1ab_0
+  - pandas=2.2.2=py310hf9f9076_1
+  - pango=1.52.2=ha41ecd1_0
   - paramiko=3.4.0=pyhd8ed1ab_0
   - pathspec=0.12.1=pyhd8ed1ab_0
   - patsy=0.5.6=pyhd8ed1ab_0
-  - pcre2=10.40=hc3806b6_0
-  - peppy=0.40.1=pyhd8ed1ab_0
-  - pillow=10.0.1=py310h29da1c1_1
+  - pcre2=10.43=hcad00b1_0
+  - peppy=0.40.2=pyhd8ed1ab_0
+  - pillow=10.3.0=py310hf73ecf8_0
   - pip=24.0=pyhd8ed1ab_0
   - pixman=0.43.2=h59595ed_0
   - pkgutil-resolve-name=1.3.10=pyhd8ed1ab_1
   - plac=1.4.3=pyhd8ed1ab_0
-  - platformdirs=4.2.0=pyhd8ed1ab_0
-  - pluggy=1.4.0=pyhd8ed1ab_0
-  - ply=3.11=py_1
+  - platformdirs=4.2.2=pyhd8ed1ab_0
+  - pluggy=1.5.0=pyhd8ed1ab_0
+  - ply=3.11=pyhd8ed1ab_2
   - prettytable=3.10.0=pyhd8ed1ab_0
-  - protobuf=4.25.2=py310ha8c1f0e_0
+  - proto-plus=1.23.0=pyhd8ed1ab_0
+  - protobuf=4.25.3=py310ha8c1f0e_0
   - psutil=5.9.8=py310h2372a71_0
   - pthread-stubs=0.4=h36c2ea0_1001
   - pulp=2.7.0=py310hff52083_1
-  - pulseaudio-client=16.1=hb77b528_5
-  - pyarrow=15.0.0=py310hf9e7431_7_cpu
-  - pyasn1=0.5.1=pyhd8ed1ab_0
-  - pyasn1-modules=0.3.0=pyhd8ed1ab_0
-  - pybigwig=0.3.22=py310h79000e5_1
-  - pybind11-abi=4=hd8ed1ab_3
-  - pycosat=0.6.6=py310h2372a71_0
-  - pycparser=2.21=pyhd8ed1ab_0
-  - pygments=2.17.2=pyhd8ed1ab_0
+  - pulseaudio-client=17.0=hb77b528_0
+  - pyarrow=16.1.0=py310h17c5347_1
+  - pyarrow-core=16.1.0=py310h6f79a3a_1_cpu
+  - pyasn1=0.6.0=pyhd8ed1ab_0
+  - pyasn1-modules=0.4.0=pyhd8ed1ab_0
+  - pybigwig=0.3.22=py310h79000e5_2
+  - pycparser=2.22=pyhd8ed1ab_0
+  - pygments=2.18.0=pyhd8ed1ab_0
   - pynacl=1.5.0=py310h2372a71_3
   - pyopenssl=24.0.0=pyhd8ed1ab_0
-  - pyparsing=3.1.1=pyhd8ed1ab_0
+  - pyparsing=3.1.2=pyhd8ed1ab_0
   - pyqt=5.15.9=py310h04931ad_5
   - pyqt5-sip=12.12.2=py310hc6cd4ac_5
   - pyranges=0.0.129=pyh7cba7a3_0
-  - pyrle=0.0.39=py310h4b81fae_0
-  - pysam=0.22.0=py310h41dec4a_0
+  - pyrle=0.0.40=py310h4b81fae_0
+  - pysam=0.22.1=py310h41dec4a_0
   - pysftp=0.2.9=py_1
   - pysocks=1.7.1=pyha2e5f31_6
-  - pytest=8.0.2=pyhd8ed1ab_0
+  - pytest=8.2.1=pyhd8ed1ab_0
   - pytest-xdist=3.5.0=pyhd8ed1ab_0
-  - python=3.10.13=hd12c33a_1_cpython
+  - python=3.10.14=hd12c33a_0_cpython
   - python-dateutil=2.9.0=pyhd8ed1ab_0
   - python-fastjsonschema=2.19.1=pyhd8ed1ab_0
-  - python-irodsclient=2.0.0=pyhd8ed1ab_0
+  - python-irodsclient=2.0.1=pyhd8ed1ab_0
   - python-tzdata=2024.1=pyhd8ed1ab_0
   - python_abi=3.10=4_cp310
   - pytz=2024.1=pyhd8ed1ab_0
   - pyu2f=0.1.5=pyhd8ed1ab_0
   - pyyaml=6.0.1=py310h2372a71_1
-  - qt-main=5.15.8=hc47bfe8_16
-  - r-base=4.3.1=h639d9d3_5
-  - rdma-core=50.0=hd3aeb46_0
+  - qt-main=5.15.8=hc9dc06e_21
+  - r-base=4.3.3=hf0d99cb_1
   - re2=2023.09.01=h7f4b329_2
   - readline=8.2=h8228510_1
-  - referencing=0.33.0=pyhd8ed1ab_0
-  - reproc=14.2.4.post0=hd590300_1
-  - reproc-cpp=14.2.4.post0=h59595ed_1
-  - requests=2.31.0=pyhd8ed1ab_0
+  - referencing=0.35.1=pyhd8ed1ab_0
+  - requests=2.32.2=pyhd8ed1ab_0
   - reretry=0.11.8=pyhd8ed1ab_0
   - rich=13.7.1=pyhd8ed1ab_0
-  - rpds-py=0.18.0=py310hcb5633a_0
+  - rpds-py=0.18.1=py310he421c4c_0
   - rsa=4.9=pyhd8ed1ab_0
-  - ruamel.yaml=0.18.6=py310h2372a71_0
-  - ruamel.yaml.clib=0.2.8=py310h2372a71_0
-  - s2n=1.4.5=h06160fa_0
-  - s3transfer=0.10.0=pyhd8ed1ab_0
-  - samtools=1.19.2=h50ea8bc_1
-  - scipy=1.12.0=py310hb13e2d6_2
-  - seaborn=0.13.2=hd8ed1ab_0
-  - seaborn-base=0.13.2=pyhd8ed1ab_0
+  - s2n=1.4.15=he19d79f_0
+  - s3transfer=0.10.1=pyhd8ed1ab_0
+  - samtools=1.20=h50ea8bc_0
+  - scipy=1.13.1=py310h93e2701_0
+  - seaborn=0.13.2=hd8ed1ab_2
+  - seaborn-base=0.13.2=pyhd8ed1ab_2
   - sed=4.8=he412f7d_0
-  - setuptools=69.1.1=pyhd8ed1ab_0
-  - setuptools-scm=8.0.4=pyhd8ed1ab_0
+  - setuptools=70.0.0=pyhd8ed1ab_0
+  - setuptools-scm=8.1.0=pyhd8ed1ab_0
   - sip=6.7.12=py310hc6cd4ac_0
   - six=1.16.0=pyh6c4a22f_0
   - slacker=0.14.0=py_0
@@ -335,18 +313,18 @@ dependencies:
   - smmap=5.0.0=pyhd8ed1ab_0
   - snakemake=7.32.4=hdfd78af_1
   - snakemake-minimal=7.32.4=pyhdfd78af_1
-  - snappy=1.1.10=h9fff704_0
+  - snappy=1.2.0=hdb0a2a9_1
   - snowballstemmer=2.2.0=pyhd8ed1ab_0
-  - sorted_nearest=0.0.39=py310h4b81fae_0
-  - sphinx=7.2.6=pyhd8ed1ab_0
+  - sorted_nearest=0.0.39=py310h4b81fae_1
+  - sphinx=7.3.7=pyhd8ed1ab_0
   - sphinxcontrib-applehelp=1.0.8=pyhd8ed1ab_0
   - sphinxcontrib-devhelp=1.0.6=pyhd8ed1ab_0
   - sphinxcontrib-htmlhelp=2.0.5=pyhd8ed1ab_0
   - sphinxcontrib-jsmath=1.0.1=pyhd8ed1ab_0
   - sphinxcontrib-qthelp=1.0.7=pyhd8ed1ab_0
   - sphinxcontrib-serializinghtml=1.1.10=pyhd8ed1ab_0
-  - statsmodels=0.14.1=py310h1f7b6fc_0
-  - stone=3.3.1=pyhd8ed1ab_0
+  - statsmodels=0.14.2=py310h261611a_0
+  - stone=3.3.6=pyhd8ed1ab_0
   - stopit=1.1.2=py_0
   - sysroot_linux-64=2.12=he073ed8_17
   - tabix=1.11=hdfd78af_0
@@ -358,20 +336,17 @@ dependencies:
   - tomli=2.0.1=pyhd8ed1ab_0
   - toposort=1.10=pyhd8ed1ab_0
   - tornado=6.4=py310h2372a71_0
-  - tqdm=4.66.2=pyhd8ed1ab_0
-  - traitlets=5.14.1=pyhd8ed1ab_0
-  - truststore=0.8.0=pyhd8ed1ab_0
-  - typing-extensions=4.10.0=hd8ed1ab_0
-  - typing_extensions=4.10.0=pyha770c72_0
+  - traitlets=5.14.3=pyhd8ed1ab_0
+  - typing-extensions=4.11.0=hd8ed1ab_0
+  - typing_extensions=4.11.0=pyha770c72_0
   - tzdata=2024a=h0c530f3_0
   - ubiquerg=0.7.0=pyhd8ed1ab_0
-  - ucx=1.15.0=h75e419f_3
   - unicodedata2=15.1.0=py310h2372a71_0
   - uritemplate=4.1.1=pyhd8ed1ab_0
-  - urllib3=2.0.7=pyhd8ed1ab_0
+  - urllib3=2.2.1=pyhd8ed1ab_0
   - veracitools=0.1.3=py_0
   - wcwidth=0.2.13=pyhd8ed1ab_0
-  - wheel=0.42.0=pyhd8ed1ab_0
+  - wheel=0.43.0=pyhd8ed1ab_1
   - wrapt=1.16.0=py310h2372a71_0
   - xcb-util=0.4.0=hd590300_1
   - xcb-util-image=0.4.0=h8ee46fc_1
@@ -382,7 +357,7 @@ dependencies:
   - xorg-kbproto=1.0.7=h7f98852_1002
   - xorg-libice=1.1.1=hd590300_0
   - xorg-libsm=1.2.4=h7391055_0
-  - xorg-libx11=1.8.7=h8ee46fc_0
+  - xorg-libx11=1.8.9=h8ee46fc_0
   - xorg-libxau=1.0.11=hd590300_0
   - xorg-libxdmcp=1.1.3=h7f98852_0
   - xorg-libxext=1.3.4=h0b41bf4_2
@@ -394,16 +369,15 @@ dependencies:
   - xorg-xproto=7.0.31=h7f98852_1007
   - xz=5.2.6=h166bdaf_0
   - yaml=0.2.5=h7f98852_2
-  - yaml-cpp=0.8.0=h59595ed_0
   - yarl=1.9.4=py310h2372a71_0
   - yte=1.5.4=pyha770c72_0
   - zipp=3.17.0=pyhd8ed1ab_0
-  - zlib=1.2.13=hd590300_5
-  - zstandard=0.22.0=py310h1275a96_0
-  - zstd=1.5.5=hfc55251_0
+  - zlib=1.2.13=h4ab18f5_6
+  - zstd=1.5.6=ha6fb4c9_0
   - pip:
+      - docutils==0.20.1
       - hic-straw==1.3.1
-      - pybind11==2.11.1
+      - pybind11==2.12.0
       - sphinx-rtd-theme==2.0.0
       - sphinxcontrib-jquery==4.1
 prefix: /oak/stanford/groups/engreitz/Users/atan5133/.conda/envs/abc-env

From 2f73fc2fbf941f910bff48b3f2e09ff5eead571c Mon Sep 17 00:00:00 2001
From: Anthony Tan <10254642+atancoder@users.noreply.github.com>
Date: Tue, 4 Jun 2024 13:00:40 -0700
Subject: [PATCH 10/10] Update circleci config.yml

---
 .circleci/config.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index d1ec5b258..5fbe3c8ba 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -21,6 +21,7 @@ jobs:
     # The executor is the environment in which the steps below will be executed
     docker:
       - image: condaforge/mambaforge
+    resource_class: large  # 8GB of memory
     # CircleCI will report the results back to your VCS provider.
     steps:
       - checkout