From a4df2c88859dc6c1742288ff8ca4f856cc74ebbd Mon Sep 17 00:00:00 2001
From: Theo Sanderson <theo@sndrsn.co.uk>
Date: Wed, 11 Oct 2023 16:34:12 +0100
Subject: [PATCH 01/10] Update AboutOverlay.jsx

---
 .../src/components/AboutOverlay.jsx           | 24 ++++++++++++++++++-
 1 file changed, 23 insertions(+), 1 deletion(-)

diff --git a/taxonium_website/src/components/AboutOverlay.jsx b/taxonium_website/src/components/AboutOverlay.jsx
index e0f58bc1..8d99f033 100644
--- a/taxonium_website/src/components/AboutOverlay.jsx
+++ b/taxonium_website/src/components/AboutOverlay.jsx
@@ -1,9 +1,31 @@
 import React, { useRef, useEffect } from "react";
 import Modal from "react-modal";
 
+const modalStyle = {
+  content: {
+    top: "50%",
+    left: "50%",
+    transform: "translate(-50%, -50%)",
+    backgroundColor: "#fafafa",
+    border: "1px solid #e2e8f0",
+    borderRadius: "8px",
+    padding: "20px",
+    maxWidth: "700px",
+    maxHeight: "80vh",
+    minWidth: "400px",
+    minHeight: "400px",
+    fontSize: "13px",
+  },
+  overlay: {
+    backgroundColor: "rgba(100, 100, 100, 0.3)",
+    zIndex: 1000,
+  },
+};
+
 function AboutOverlay({ enabled, setEnabled, overlayContent }) {
   return (
-    <Modal isOpen={enabled} onRequestClose={() => setEnabled(false)}>
+    <Modal isOpen={enabled} onRequestClose={() => setEnabled(false)}
+      style={modalStyle}>
       <button
         className="absolute text-lg font-bold top-0 right-0 m-2"
         onClick={() => setEnabled(false)}

From 39947b1f96d0674d238b0162363b5c5071695718 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 11 Oct 2023 15:35:49 +0000
Subject: [PATCH 02/10] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 taxonium_website/src/components/AboutOverlay.jsx | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/taxonium_website/src/components/AboutOverlay.jsx b/taxonium_website/src/components/AboutOverlay.jsx
index 8d99f033..353233ea 100644
--- a/taxonium_website/src/components/AboutOverlay.jsx
+++ b/taxonium_website/src/components/AboutOverlay.jsx
@@ -24,8 +24,11 @@ const modalStyle = {
 
 function AboutOverlay({ enabled, setEnabled, overlayContent }) {
   return (
-    <Modal isOpen={enabled} onRequestClose={() => setEnabled(false)}
-      style={modalStyle}>
+    <Modal
+      isOpen={enabled}
+      onRequestClose={() => setEnabled(false)}
+      style={modalStyle}
+    >
       <button
         className="absolute text-lg font-bold top-0 right-0 m-2"
         onClick={() => setEnabled(false)}

From 92599c6296928d585f0a791ae7a1f24a7aef38a1 Mon Sep 17 00:00:00 2001
From: Theo Sanderson <theo@sndrsn.co.uk>
Date: Wed, 11 Oct 2023 16:46:25 +0100
Subject: [PATCH 03/10] Update AboutOverlay.jsx

---
 taxonium_website/src/components/AboutOverlay.jsx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/taxonium_website/src/components/AboutOverlay.jsx b/taxonium_website/src/components/AboutOverlay.jsx
index 353233ea..21909172 100644
--- a/taxonium_website/src/components/AboutOverlay.jsx
+++ b/taxonium_website/src/components/AboutOverlay.jsx
@@ -62,8 +62,8 @@ function AboutOverlay({ enabled, setEnabled, overlayContent }) {
             project.
           </p>
 
-          <p className="mb-1 text-sm mt-6 text-sm text-gray-700">
-            <h3 className="font-bold text-md">Citation</h3>
+          <p className="mb-1  mt-6 text-sm text-gray-700">
+            <h3 className="font-bold">Citation</h3>
             If you use Taxonium in your research, please cite:
             <br />
             Theo Sanderson (2022){" "}

From 38084f2510262344262ab7269ebfae0d4990c86d Mon Sep 17 00:00:00 2001
From: Theo Sanderson <theo@sndrsn.co.uk>
Date: Wed, 11 Oct 2023 16:52:00 +0100
Subject: [PATCH 04/10] Update AboutOverlay.jsx

---
 taxonium_website/src/components/AboutOverlay.jsx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/taxonium_website/src/components/AboutOverlay.jsx b/taxonium_website/src/components/AboutOverlay.jsx
index 21909172..b01df8a6 100644
--- a/taxonium_website/src/components/AboutOverlay.jsx
+++ b/taxonium_website/src/components/AboutOverlay.jsx
@@ -62,7 +62,7 @@ function AboutOverlay({ enabled, setEnabled, overlayContent }) {
             project.
           </p>
 
-          <p className="mb-1  mt-6 text-sm text-gray-700">
+          <p className="mb-1  mt-6 text-gray-700">
             <h3 className="font-bold">Citation</h3>
             If you use Taxonium in your research, please cite:
             <br />

From 0db8b0747cd06d08dd6e3fabd2b6794dad4cb8ae Mon Sep 17 00:00:00 2001
From: Theo Sanderson <theo@sndrsn.co.uk>
Date: Wed, 11 Oct 2023 16:53:56 +0100
Subject: [PATCH 05/10] Rename docker-publish-frontend.yml to
 docker-publish-frontend.yml_disabled

---
 ...-publish-frontend.yml => docker-publish-frontend.yml_disabled} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename .github/workflows/{docker-publish-frontend.yml => docker-publish-frontend.yml_disabled} (100%)

diff --git a/.github/workflows/docker-publish-frontend.yml b/.github/workflows/docker-publish-frontend.yml_disabled
similarity index 100%
rename from .github/workflows/docker-publish-frontend.yml
rename to .github/workflows/docker-publish-frontend.yml_disabled

From 774f9a7d39c242a0ec972d874ab4c06dee1bbd9b Mon Sep 17 00:00:00 2001
From: Theo Sanderson <theo@sndrsn.co.uk>
Date: Wed, 11 Oct 2023 16:55:16 +0100
Subject: [PATCH 06/10] Delete .github/selenium_tests directory

---
 .github/selenium_tests/selenium_tests.py | 42 ------------------------
 1 file changed, 42 deletions(-)
 delete mode 100644 .github/selenium_tests/selenium_tests.py

diff --git a/.github/selenium_tests/selenium_tests.py b/.github/selenium_tests/selenium_tests.py
deleted file mode 100644
index 9c6a8b5a..00000000
--- a/.github/selenium_tests/selenium_tests.py
+++ /dev/null
@@ -1,42 +0,0 @@
-from selenium import webdriver
-from selenium import webdriver
-from webdriver_manager.chrome import ChromeDriverManager
-
-driver = webdriver.Chrome(ChromeDriverManager().install())
-from selenium.webdriver.chrome.options import Options
-from selenium.webdriver.chrome.service import Service
-from selenium.webdriver.support.ui import WebDriverWait
-from selenium.webdriver.support import expected_conditions as EC
-import time
-import sys
-
-url = sys.argv[1]
-
-chrome_service = Service(
-    ChromeDriverManager(chrome_type=ChromeType.CHROMIUM).install())
-
-chrome_options = Options()
-options = [
-    "--headless", "--disable-gpu", "--window-size=1920,1200",
-    "--ignore-certificate-errors", "--disable-extensions", "--no-sandbox",
-    "--disable-dev-shm-usage", "--disable-web-security"
-]
-for option in options:
-    chrome_options.add_argument(option)
-
-driver = webdriver.Chrome(service=chrome_service, options=chrome_options)
-
-#driver.get('http://nytimes.com')
-
-driver.get(url)
-
-print(url)
-print("###")
-time.sleep(20)
-
-print(driver.get_log("browser"))
-
-if driver.find_elements_by_css_selector('#view-main'):
-    print("Element exists")
-else:
-    raise ValueError("Could not find element")

From 0d392354a4542b284c4bb002ca2df60410411c3c Mon Sep 17 00:00:00 2001
From: Theo Sanderson <theo@sndrsn.co.uk>
Date: Wed, 11 Oct 2023 17:18:11 +0100
Subject: [PATCH 07/10] cleanup fails

---
 .../docker-publish-frontend.yml_disabled      | 80 -------------------
 .github/workflows/integration-test.yml        | 18 -----
 2 files changed, 98 deletions(-)
 delete mode 100644 .github/workflows/docker-publish-frontend.yml_disabled
 delete mode 100644 .github/workflows/integration-test.yml

diff --git a/.github/workflows/docker-publish-frontend.yml_disabled b/.github/workflows/docker-publish-frontend.yml_disabled
deleted file mode 100644
index 466a409a..00000000
--- a/.github/workflows/docker-publish-frontend.yml_disabled
+++ /dev/null
@@ -1,80 +0,0 @@
-name: Docker publish frontend
-
-# This workflow uses actions that are not certified by GitHub.
-# They are provided by a third-party and are governed by
-# separate terms of service, privacy policy, and support
-# documentation.
-
-on:
-  repository_dispatch:
-  workflow_dispatch:
-  schedule:
-    - cron: "37 18 * * *"
-  push:
-    branches: [master]
-    # Publish semver tags as releases.
-    tags: ["v*.*.*"]
-  pull_request:
-    branches: [master]
-
-env:
-  # Use docker.io for Docker Hub if empty
-  REGISTRY: docker.io
-  # github.repository as <account>/<repo>
-  IMAGE_NAME: theosanderson/taxonium_frontend
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      packages: write
-      # This is used to complete the identity challenge
-      # with sigstore/fulcio when running outside of PRs.
-      id-token: write
-
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v3
-
-      # Install the cosign tool except on PR
-      # https://github.com/sigstore/cosign-installer
-      - name: Install cosign
-        if: github.event_name != 'pull_request'
-        uses: sigstore/cosign-installer@d6a3abf1bdea83574e28d40543793018b6035605
-        with:
-          cosign-release: "v1.7.1"
-
-      # Workaround: https://github.com/docker/build-push-action/issues/461
-      - name: Setup Docker buildx
-        uses: docker/setup-buildx-action@79abd3f86f79a9d68a23c75a09a9a85889262adf
-
-      # Login against a Docker registry except on PR
-      # https://github.com/docker/login-action
-      - name: Log into registry ${{ env.REGISTRY }}
-        if: github.event_name != 'pull_request'
-        uses: docker/login-action@28218f9b04b4f3f62068d7b6ce6ca5b26e35336c
-        with:
-          registry: ${{ env.REGISTRY }}
-          username: theosanderson
-          password: ${{ secrets.DOCKER_TOKEN }}
-
-      # Extract metadata (tags, labels) for Docker
-      # https://github.com/docker/metadata-action
-      - name: Extract Docker metadata
-        id: meta
-        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
-        with:
-          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
-
-      # Build and push Docker image with Buildx (don't push on PR)
-      # https://github.com/docker/build-push-action
-      - name: Build and push Docker image
-        id: build-and-push
-        uses: docker/build-push-action@ac9327eae2b366085ac7f6a2d02df8aa8ead720a
-        with:
-          context: .
-          file: ./Dockerfile.frontend
-          push: ${{ github.event_name != 'pull_request' }}
-          tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml
deleted file mode 100644
index 71571fbe..00000000
--- a/.github/workflows/integration-test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-name: Integration Test
-
-on:
-  repository_dispatch:
-  workflow_dispatch:
-  push:
-  pull_request:
-    branches: [master]
-  schedule:
-    - cron: "0 0 * * *"
-jobs:
-  build:
-    uses: ./.github/workflows/frontend-test.yml
-  python:
-    uses: ./.github/workflows/python-test.yml
-  # selenium:
-  #   needs: [build, python]
-  #   uses: ./.github/workflows/selenium-test.yml

From 653a53720eeb2d230db377ad3c93d9c1fca53ef7 Mon Sep 17 00:00:00 2001
From: Theo Sanderson <theo@sndrsn.co.uk>
Date: Wed, 11 Oct 2023 17:19:01 +0100
Subject: [PATCH 08/10] only trigger electron release on.. release!

---
 .github/workflows/electron-build.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/electron-build.yml b/.github/workflows/electron-build.yml
index 9601e379..995f42f5 100644
--- a/.github/workflows/electron-build.yml
+++ b/.github/workflows/electron-build.yml
@@ -1,8 +1,6 @@
 name: Electron build/release
 
 on:
-  push:
-  pull_request:
   release:
     types:
       - created

From 323033d478f5d168b517ff3bf428fdede67445e1 Mon Sep 17 00:00:00 2001
From: Theo Sanderson <theo@sndrsn.co.uk>
Date: Wed, 11 Oct 2023 17:19:19 +0100
Subject: [PATCH 09/10] update

---
 .github/workflows/{electron-build.yml => electron-release.yml} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename .github/workflows/{electron-build.yml => electron-release.yml} (100%)

diff --git a/.github/workflows/electron-build.yml b/.github/workflows/electron-release.yml
similarity index 100%
rename from .github/workflows/electron-build.yml
rename to .github/workflows/electron-release.yml

From 600f36efb57d43690f66429bd2def458a380a5fc Mon Sep 17 00:00:00 2001
From: Theo Sanderson <theo@sndrsn.co.uk>
Date: Wed, 11 Oct 2023 17:22:41 +0100
Subject: [PATCH 10/10] up

---
 .github/workflows/selenium-test.yml | 43 -----------------------------
 1 file changed, 43 deletions(-)
 delete mode 100644 .github/workflows/selenium-test.yml

diff --git a/.github/workflows/selenium-test.yml b/.github/workflows/selenium-test.yml
deleted file mode 100644
index caf8a673..00000000
--- a/.github/workflows/selenium-test.yml
+++ /dev/null
@@ -1,43 +0,0 @@
-name: Selenium
-
-on:
-  workflow_call:
-
-jobs:
-  test:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - name: Installed package list
-        run: apt list --installed
-      - uses: actions/download-artifact@v3
-        with:
-          name: tfci-taxonium-config
-          path: ./data/
-      - uses: actions/download-artifact@v3
-        with:
-          name: taxonium_website_build
-          path: ./web/
-      - uses: actions/setup-python@v3
-        with:
-          python-version: "3.8"
-      - name: Start server
-        run: python -m http.server &
-        working-directory: ./web/
-      - name: Start server
-        run: |
-          ls
-          python -m http.server 3000 &
-        working-directory: ./data/
-      - name: Installed package list
-        run: apt list --installed
-      - name: Remove Chrome
-        run: sudo apt purge google-chrome-stable
-      - name: Remove default Chromium
-        run: sudo apt purge chromium-browser
-      - name: Install a new Chromium
-        run: sudo apt install -y chromium-browser
-      - name: Install all necessary packages
-        run: pip install requests beautifulsoup4 pandas webdriver-manager selenium
-      - name: Run the selenium script
-        run: python .github/selenium_tests/selenium_tests.py "http://localhost:8000/?protoUrl=http://localhost:3000/tfci-taxonium-config.jsonl.gz"