From 1dcf9495e6b86ae029bc9933a1f4523fddade759 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi <sasha99250@gmail.com>
Date: Mon, 2 Oct 2023 22:33:39 +0200
Subject: [PATCH 1/2] Fixed #227

---
 pephub/helpers.py | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/pephub/helpers.py b/pephub/helpers.py
index 34070f50..053a2a92 100644
--- a/pephub/helpers.py
+++ b/pephub/helpers.py
@@ -9,6 +9,7 @@
 from yaml import safe_load
 import zipfile
 import io
+import yaml
 
 import peppy
 from peppy.const import SAMPLE_DF_KEY
@@ -130,20 +131,24 @@ def zip_pep(project: peppy.Project) -> Response:
     if project.config:
         prj_cof_file = project.config_file or "config.yaml"
         cfg_filename_base = basename(prj_cof_file)
-        content_to_zip[cfg_filename_base] = project.config.to_yaml()
+        content_to_zip[cfg_filename_base] = yaml.dump(project.config, indent=4)
 
     if project.sample_table is not None:
         sample_table_filename = basename(
             project.to_dict().get("sample_table", "sample_table.csv")
         )
-        content_to_zip[sample_table_filename] = project[SAMPLE_DF_KEY].to_csv()
+        content_to_zip[sample_table_filename] = project[SAMPLE_DF_KEY].to_csv(
+            index=False
+        )
 
     if project.subsample_table is not None:
         if not isinstance(project.subsample_table, list):
             subsample_table_filename = basename(
                 project.to_dict().get("subsample_table", "subsample_table.csv")
             )
-            content_to_zip[subsample_table_filename] = project.subsample_table.to_csv()
+            content_to_zip[subsample_table_filename] = project.subsample_table.to_csv(
+                index=False
+            )
         else:
             subsample_table_filenames = project.to_dict().get(
                 "subsample_table", "subsample_table.csv"
@@ -152,7 +157,7 @@ def zip_pep(project: peppy.Project) -> Response:
                 project.subsample_table, subsample_table_filenames
             ):
                 subsample_table_filename = basename(sstable_filename)
-                content_to_zip[subsample_table_filename] = sstable.to_csv()
+                content_to_zip[subsample_table_filename] = sstable.to_csv(index=False)
 
     zip_filename = project.name or f"downloaded_pep_{date.today()}"
     return zip_conv_result(content_to_zip, filename=zip_filename)

From 772f50d76ab4171a12b7d41e49290810b194009e Mon Sep 17 00:00:00 2001
From: Khoroshevskyi <sasha99250@gmail.com>
Date: Mon, 2 Oct 2023 22:41:10 +0200
Subject: [PATCH 2/2] changelog

---
 docs/changelog.md                 | 6 ++++++
 pephub/_version.py                | 2 +-
 requirements/requirements-all.txt | 2 +-
 3 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/docs/changelog.md b/docs/changelog.md
index dbff0948..dd448749 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -2,6 +2,12 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
+# [0.10.4] - 10-02-2023
+
+### Fixed
+
+- PEP zip downloading
+
 # [0.10.3] - 08-31-2023
 
 ### Changed
diff --git a/pephub/_version.py b/pephub/_version.py
index b2385cb4..d9b054ab 100644
--- a/pephub/_version.py
+++ b/pephub/_version.py
@@ -1 +1 @@
-__version__ = "0.10.3"
+__version__ = "0.10.4"
diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
index ca405b5b..33d32f40 100644
--- a/requirements/requirements-all.txt
+++ b/requirements/requirements-all.txt
@@ -9,7 +9,7 @@ tqdm
 uvicorn
 python-dotenv
 pepdbagent>=0.6.0
-peppy<=0.40.0a4
+peppy>=0.40.0a4
 qdrant-client
 requests
 aiofiles