From 8ca49a96804d5f58ba3704961c4607aa9f80b53d Mon Sep 17 00:00:00 2001
From: Chris Rosenthal <crosenth@uw.edu>
Date: Fri, 9 Aug 2024 22:41:18 -0700
Subject: [PATCH] cleaning up dependencies with no pinning and using cronjob to
 test dependencies monthly

---
 Dockerfile       |  5 ++---
 requirements.txt | 40 ++++++++++------------------------------
 2 files changed, 12 insertions(+), 33 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 26adead..52eb603 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -13,14 +13,13 @@ RUN mkdir /usr/local/share/deenurp/
 COPY bin /usr/local/share/deenurp/bin
 COPY tests /usr/local/share/deenurp/tests
 COPY deenurp /usr/local/share/deenurp/deenurp
-COPY deenurp.py setup.py requirements.txt /usr/local/share/deenurp/
+COPY deenurp.py setup.py /usr/local/share/deenurp/
 
 # Install deenurp and dependencies
 RUN cd /usr/local/share/deenurp/ && \
     PYTHON=/usr/local/bin/python3 \
     DEENURP=/usr/local/share/deenurp/ \
-    bin/bootstrap.sh /usr/local/ \
-    pip install --requirement requirements.txt
+    bin/bootstrap.sh /usr/local/
 
 # clean up sources apt packages
 RUN rm -rf /var/lib/apt/lists/* && \
diff --git a/requirements.txt b/requirements.txt
index f787e8f..c639761 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,30 +1,10 @@
-biopython==1.84
-Cython==3.0.11
-decorator==5.1.1
-DendroPy==5.0.1
-fastalite==0.4.1
-greenlet==3.0.3
-hdbscan==0.8.38.post1
-Jinja2==3.1.4
-joblib==1.4.2
-MarkupSafe==2.1.5
-numpy==2.0.1
-packaging==24.1
-pandas==2.2.2
-psycopg==3.2.1
-psycopg-binary==3.2.1
-psycopg2-binary==2.9.9
-pygtrie==2.5.0
-python-dateutil==2.9.0.post0
-pytz==2024.1
-PyYAML==6.0.2
-scikit-learn==1.5.1
-scipy==1.14.0
-seqmagick==0.8.6
-six==1.16.0
-SQLAlchemy==2.0.32
-sqlparse==0.5.1
-taxtastic==0.10.0
-threadpoolctl==3.5.0
-typing_extensions==4.12.2
-tzdata==2024.1
+biopython
+hdbscan
+numpy
+packaging
+pandas
+scikit-learn
+scipy
+sqlalchemy
+seqmagick
+taxtastic