feat: various additions and fixes

.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff

.github/workflows/formatting.yml

@@ -0,0 +1,18 @@
+name: Formatting
+
+on:
+  pull_request:
+    branches: [main]
+
+jobs:
+  formatting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: prefix-dev/setup-pixi@v0
+        with:
+          cache: true
+
+      - name: formatting
+        run: pixi run check-nbs

.gitignore

@@ -2,3 +2,6 @@
 exercises/*
 templates/*.html
 templates/*_files
+# pixi environments
+.pixi/*
+!.pixi/config.toml

lessons/lesson_01.ipynb

@@ -181,7 +181,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(\"Hello World!\") # Code before the hash sign will be executed"
+    "print(\"Hello World!\")  # Code before the hash sign will be executed"
    ]
   },
   {
@@ -210,7 +210,7 @@
    "source": [
     "a = 3\n",
     "b = 5\n",
-    "a + b**2 # this means to the power of 2"
+    "a + b**2  # this means to the power of 2"
    ]
   },
   {
@@ -322,7 +322,7 @@
    "outputs": [],
    "source": [
     "a = 2  # int\n",
-    "b = 3.14 # float\n",
+    "b = 3.14  # float\n",
     "\n",
     "print(\"a is of type\", type(a))\n",
     "print(\"b is of type\", type(b))\n",
@@ -419,8 +419,8 @@
    "outputs": [],
    "source": [
     "# Note how we are using a list defined above in a prior Jupyter cell!\n",
-    "print(list_num[2]) # indexing\n",
-    "print(list_num[1:3]) # slicing\n",
+    "print(list_num[2])  # indexing\n",
+    "print(list_num[1:3])  # slicing\n",
     "# Note how we are using a list defined above in a prior Jupyter cell!\\n"
    ]
   },
@@ -557,7 +557,7 @@
     "import numpy as np\n",
     "\n",
     "# series of numbers defined by start, stop, step\n",
-    "x = np.arange(0, 4*np.pi, 0.1)\n",
+    "x = np.arange(0, 4 * np.pi, 0.1)\n",
     "y = np.sin(x)\n",
     "plt.plot(x, y)\n",
     "plt.show()"
@@ -630,7 +630,7 @@
     "# what is wrong here? Fix it.\n",
     "\n",
     "a = 12\n",
-    "b = '23'\n",
+    "b = \"23\"\n",
     "print(a + b)"
    ]
   },
@@ -655,7 +655,7 @@
    "outputs": [],
    "source": [
     "# Solution\n",
-    "a = 30\n"
+    "a = 30"
    ]
   },
   {
@@ -671,7 +671,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Solution\n"
+    "# Solution"
    ]
   },
   {
@@ -688,7 +688,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Solution\n"
+    "# Solution"
    ]
   },
   {
@@ -706,7 +706,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Solution\n"
+    "# Solution"
    ]
   }
  ],

lessons/lesson_02.ipynb

@@ -587,12 +587,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "seq = 'GTACCTTGATTTCGTAA'\n",
+    "seq = \"GTACCTTGATTTCGTAA\"\n",
     "\n",
-    "print(seq.find('GTA'))\n",
-    "print(seq.find('CCT'))\n",
-    "print(seq.find('GTA', 1))\n",
-    "print(seq.find('GTA', 1, 10))"
+    "print(seq.find(\"GTA\"))\n",
+    "print(seq.find(\"CCT\"))\n",
+    "print(seq.find(\"GTA\", 1))\n",
+    "print(seq.find(\"GTA\", 1, 10))"
    ]
   },
   {
@@ -608,7 +608,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(seq.rfind('TTT'))"
+    "print(seq.rfind(\"TTT\"))"
    ]
   },
   {
@@ -624,7 +624,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "seq.count('TA')"
+    "seq.count(\"TA\")"
    ]
   },
   {
@@ -667,8 +667,8 @@
     "print(seq.strip(\"T\"))  # removes nothing\n",
     "print(seq.lstrip(\"TAGC\"))  # removes all leading letters matching the query\n",
     "print(seq.rstrip(\"tagc\"))  # removes all trailing letters matching the query\n",
-    "print(seq.removeprefix(\"GtAc\")) # removes exact prefix\n",
-    "print(seq.removesuffix(\"GTaa\")) # removes exact suffix"
+    "print(seq.removeprefix(\"GtAc\"))  # removes exact prefix\n",
+    "print(seq.removesuffix(\"GTaa\"))  # removes exact suffix"
    ]
   },
   {
@@ -786,8 +786,7 @@
     "# whole divider\n",
     "\n",
     "\n",
-    "# Remainder\n",
-    "\n"
+    "# Remainder"
    ]
   },
   {
@@ -818,7 +817,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Solution\n"
+    "# Solution"
    ]
   },
   {
@@ -848,7 +847,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Solution\n"
+    "# Solution"
    ]
   }
  ],

lessons/lesson_03.ipynb

@@ -443,7 +443,7 @@
    "source": [
     "# Solution\n",
     "dna1 = \"ATTATTAGGACCACA\"\n",
-    "dna2 = \"ATTATTAGGAACACA\"\n"
+    "dna2 = \"ATTATTAGGAACACA\""
    ]
   },
   {
@@ -461,7 +461,7 @@
    "source": [
     "# Solution\n",
     "seq1 = \"ACGTAGCTAGCTAGCTAGCTA\"\n",
-    "seq2 = \"GTGCATGCTAGCTAGCTAGCA\"\n"
+    "seq2 = \"GTGCATGCTAGCTAGCTAGCA\""
    ]
   },
   {
@@ -479,7 +479,7 @@
    "outputs": [],
    "source": [
     "# Solution\n",
-    "seq = \"ATGGACGTAGTCGGCCCGTGAAAGCGATCGATCG\"\n"
+    "seq = \"ATGGACGTAGTCGGCCCGTGAAAGCGATCGATCG\""
    ]
   },
   {
@@ -505,7 +505,7 @@
    "source": [
     "# Solution\n",
     "seq1 = \"GGCTATGCCGCCGTTATACTCGAGACTAAGTAGTC\"\n",
-    "seq2 = \"GGCTATGCCGCCGTTATATCGAGACTAAAGTAGTC\"\n"
+    "seq2 = \"GGCTATGCCGCCGTTATATCGAGACTAAAGTAGTC\""
    ]
   },
   {
@@ -522,7 +522,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Solution\n"
+    "# Solution"
    ]
   },
   {
@@ -539,11 +539,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Solution\n"
+    "# Solution"
    ]
   }
  ],
-  "metadata": {
+ "metadata": {
   "celltoolbar": "Slideshow",
   "kernelspec": {
    "display_name": "python-course",