Remove pipenv and pin requirements

.circleci/config.yml

@@ -2,7 +2,7 @@ version: 2
 jobs:
   test_python:
     docker:
-      - image: themattrix/tox
+      - image: cimg/python:3.8
       - image: viime/opencpu-base
         command: |
           /bin/sh -c "chmod a+w /usr/local/lib/R/site-library && service cron start && /usr/lib/rstudio-server/bin/rserver && apachectl -DFOREGROUND"
@@ -13,12 +13,12 @@ jobs:
           command: |
             echo "repo=\"girder/viime\"&subdir=\"devops/viime\"&ref=\"${CIRCLE_SHA1}\"&dependencies=NA&upgrade=\"never\"" > input.txt
             curl http://localhost:8004/ocpu/library/devtools/R/install_github/ -d "@input.txt"
-      - run: pip install -U 'tox>=3.7'
-#       - run: tox -p auto -o
+      - run: pip install tox
+      - run: tox -p auto -o
 
   test_web:
     docker:
-      - image: circleci/node:12
+      - image: cimg/python:3.8-node
     steps:
       - checkout
       - restore_cache:
@@ -46,7 +46,7 @@ jobs:
 
   test_e2e:
     docker:
-      - image: circleci/python:3.6-node-browsers
+      - image: cimg/python:3.8-browsers
       - image: viime/opencpu-base
         command: |
           /bin/sh -c "chmod a+w /usr/local/lib/R/site-library && service cron start && /usr/lib/rstudio-server/bin/rserver && apachectl -DFOREGROUND"
@@ -98,7 +98,7 @@ jobs:
 
   release:
     docker:
-      - image: node:12
+      - image: cimg/python:3.8-node
     steps:
       - checkout
       - restore_cache:
@@ -118,7 +118,6 @@ jobs:
       - run:
           name: Build python package
           command: |
-            curl https://bootstrap.pypa.io/pip/2.7/get-pip.py | python
             pip install tox
             tox -e release
       - run:
@@ -131,7 +130,7 @@ jobs:
 
   publish:
     docker:
-      - image: circleci/buildpack-deps:stretch
+      - image: cimg/base:current
     steps:
       - checkout
       - setup_remote_docker:
@@ -146,7 +145,7 @@ jobs:
 
   deploy:
     docker:
-      - image: circleci/python:3.6.1
+      - image: cimg/python:3.8
     environment:
       AWS_DEFAULT_OUTPUT: json
     steps:

README.md

@@ -5,19 +5,9 @@ VIIME
 
 Getting started (Running natively)
 ----------------------------------
-
-This project includes a `Pipfile` to help set up a virtual environment for
-VIIME. To set up the virtual environment
-
-```sh
-pipenv install
-```
-
-and to enter it
-
-```sh
-pipenv shell
-```
+To install for development:
+* [Create and activate a virtual environment](https://docs.python.org/3/tutorial/venv.html) 
+* Install the dependencies with `pip install -r requirements.txt`
 
 VIIME is configured from a `.env` file present in the current directory where
 it is executed.  See the included [.env_example](./.env_example) for an example

devops/ansible/site.yml

@@ -64,7 +64,6 @@
           - wheel
         state: "latest"
         virtualenv: "{{ venv }}"
-        virtualenv_command: "{{ ansible_python_interpreter }} -m venv"
       become: true
       become_user: gunicorn
 
@@ -73,23 +72,29 @@
         name: "gunicorn"
         state: "present"
         virtualenv: "{{ venv }}"
-        virtualenv_command: "{{ ansible_python_interpreter }} -m venv"
       notify: Restart gunicorn
       become: true
       become_user: gunicorn
 
+    # TODO: It'd probably be better to clone the repo (which is public) and directly install it
+    # here, rather than depend on an sdist being pre-built by CI.
     - name: Copy viime sdist to the remote machine
       copy:
         src: "{{ viime_sdist_path }}"
         dest: "/tmp/viime-sdist.tar.gz"
 
+    - name: Copy requirements.txt
+      copy:
+        src: "{{ playbook_dir }}/../../requirements.txt"
+        dest: "/tmp/requirements.txt"
+
     - name: Install viime python package
       pip:
         name: "/tmp/viime-sdist.tar.gz[memcached,sentry]"
+        requirements: "/tmp/requirements.txt"
         state: "forcereinstall"
         extra_args: "--no-cache-dir"
         virtualenv: "{{ venv }}"
-        virtualenv_command: "{{ ansible_python_interpreter }} -m venv"
       notify:
         - Migrate database
         - Restart gunicorn
@@ -99,9 +104,9 @@
 
     - name: Add gunicorn environment variables
       template:
-          src: "home/gunicorn/.gunicorn_env"
-          dest: "/home/gunicorn/.env"
-          mode: 0600
+        src: "home/gunicorn/.gunicorn_env"
+        dest: "/home/gunicorn/.env"
+        mode: 0600
       become: true
       become_user: gunicorn
 

requirements.txt

@@ -0,0 +1,53 @@
+alembic==1.5.6
+blinker==1.4
+certifi==2020.12.5
+chardet==4.0.0
+click==7.1.2
+cycler==0.10.0
+decorator==4.4.2
+dogpile.cache==1.1.2
+et-xmlfile==1.0.1
+Flask==1.1.2
+Flask-Cors==3.0.10
+Flask-Migrate==2.7.0
+Flask-SQLAlchemy==2.4.4
+gunicorn==19.9.0
+idna==2.10
+importlib-metadata==3.7.2
+itsdangerous==1.1.0
+Jinja2==2.11.3
+joblib==1.0.1
+kiwisolver==1.3.1
+Mako==1.1.4
+MarkupSafe==1.1.1
+marshmallow==3.10.0
+matplotlib==3.3.4
+numpy==1.19.5
+openpyxl==3.0.7
+packaging==20.4
+pandas==1.1.5
+pbr==5.5.1
+Pillow==8.1.2
+pylibmc==1.6.1
+pyparsing==2.4.7
+python-dateutil==2.8.1
+python-dotenv==0.15.0
+python-editor==1.0.4
+pytz==2021.1
+requests==2.25.1
+scikit-learn==0.24.1
+scipy==1.5.4
+sentry-sdk==1.0.0
+six==1.15.0
+sklearn==0.0
+SQLAlchemy==1.3.23
+SQLAlchemy-Utils==0.36.8
+stevedore==3.3.0
+threadpoolctl==2.1.0
+typing-extensions==3.7.4.3
+urllib3==1.26.3
+viime==1.0.1
+webargs==5.5.3
+Werkzeug==1.0.1
+xlrd==1.2.0
+zipp==3.4.1

setup.py

@@ -28,6 +28,7 @@ def list_files_recursive(relpath):
     author_email='[email protected]',
     packages=find_packages(include=['viime']),
     include_package_data=True,
+    python_requires='>=3.8',
     install_requires=[
         'alembic',
         'dogpile.cache',

tests/test_excel_file_api.py

@@ -16,7 +16,7 @@ def test_upload_excel_file(client):
 
     assert resp.status_code == 201
     res = resp.json
-    assert type(res) == list
+    assert type(res) is list
     assert len(res) == 2
 
     sheet1 = res[0]

tox.ini

@@ -1,25 +1,27 @@
 [tox]
-envlist = py3{6,7,8}, lint
-skip_missing_interpreters = true
+envlist = py38, lint
+basepython = python3.8
 
 [testenv]
-deps = httmock
-       pytest
-       pytest-cov
+deps =
+    -r requirements.txt
+    httmock
+    pytest
+    pytest-cov
 commands = pytest {posargs} tests
 usedevelop = true
 
 [testenv:lint]
-deps = flake8
-       flake8-import-order
-       flake8-quotes
-       pep8-naming
+deps =
+    flake8
+    flake8-import-order
+    flake8-quotes
+    pep8-naming
 commands = flake8 {posargs} setup.py tests viime
 
 [testenv:release]
 skip_install = true
 skipsdist = true
-basepython = python2.7
 commands = python setup.py sdist
 
 [testenv:mypy]

viime/views.py

@@ -12,7 +12,7 @@
 from werkzeug.datastructures import FileStorage
 
 from viime import opencpu, samples
-from viime.analyses import anova_test, factor_analysis, hierarchical_clustering,\
+from viime.analyses import anova_test, factor_analysis, hierarchical_clustering, \
     oplsda, pairwise_correlation, plsda, roc_analysis, wilcoxon_test
 from viime.imputation import IMPUTE_MCAR_METHODS, IMPUTE_MNAR_METHODS
 from viime.models import AXIS_NAME_TYPES, clean, CSVFile, CSVFileSchema, db, \