Add language tags to docs code blocks

scbirlab · May 16, 2023 · 995a65f · 995a65f
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diff --git a/README.md b/README.md
@@ -8,15 +8,15 @@ Python utilities for working with nucleotide sequence strings.
 
 Install the pre-compiled version from PyPI:
 
-```
+```bash
 pip install streq
 ```
 
 ### From source
 
 Clone the repository, then `cd` into it. Then run:
 
-```
+```bash
 pip install -e .
 ```
 
@@ -29,7 +29,7 @@ Sequences can be upper or lower case, and case will be preserved through transfo
 
 Reverse complement.
 
-```
+```python
 >>> import streq as sq
 >>>
 >>> sq.reverse_complement('ATCG')
@@ -38,7 +38,7 @@ Reverse complement.
 
 Convert between RNA and DNA alphabets.
 
-```
+```python
 >>> sq.to_rna('ATCG')
 'AUCG'
 >>> sq.to_dna('AUCG')
@@ -47,7 +47,7 @@ Convert between RNA and DNA alphabets.
 
 Slice circular sequences such as plasmids or bacterial genomes.
 
-```
+```python
 >>> sq.Circular('ATCG')[-1:3]
 'GATC'
 >>> sq.reverse_complement(sq.Circular('ATCG'))[-1:3]
@@ -56,7 +56,7 @@ Slice circular sequences such as plasmids or bacterial genomes.
 
 Cases are preserved throughout the transformations.
 
-```
+```python
 >>> sq.reverse_complement(sq.Circular('ATCg'))
 'cGAT'
 ```
@@ -65,7 +65,7 @@ Cases are preserved throughout the transformations.
 
 Get GC and pyrimidine content.
 
-```
+```python
 >>> sq.gc_content('AGGG')
 0.75
 >>> sq.pyrimidine_content('AUGGG')
@@ -74,7 +74,7 @@ Get GC and pyrimidine content.
 
 Get autocorrelation (rough indicator for secondary structure).
 
-```
+```python
 >>> sq.correlation('AACC')
 0.0
 >>> sq.correlation('AAATTT')
@@ -87,7 +87,7 @@ Get autocorrelation (rough indicator for secondary structure).
 
 Provide a second sequence to get correlation between sequences.
 
-```
+```python
 >>> sq.correlation('AAA', 'TTT')
 0.0
 >>> sq.correlation('AAA', 'AAA')
@@ -98,7 +98,7 @@ Provide a second sequence to get correlation between sequences.
 
 Calculate Levenshtein (insert, delete, mutate) distance.
 
-```
+```python
 >>> sq.levenshtein('AAATTT', 'AAATTT')
 0
 >>> sq.levenshtein('AAATTT', 'ACTTT')
@@ -109,7 +109,7 @@ Calculate Levenshtein (insert, delete, mutate) distance.
 
 Calculate Hamming (mismatch) distance.
 
-```
+```python
 >>> sq.hamming('AAA', 'ATA')
 1
 >>> sq.hamming('AAA', 'ATT')
@@ -122,7 +122,7 @@ Calculate Hamming (mismatch) distance.
 
 Search sequences using IUPAC symbols and iterate through the results.
 
-```
+```python
 >>> for (start, end), match in sq.find_iupac('ARY', 'AATAGCAGTGTGAAC'):
 ...     print(f"Found ARY at {start}:{end}: {match}")
 ... 
@@ -134,7 +134,7 @@ Found ARY at 12:15: AAC
 
 Find common Type IIS restriction sites:
 
-```
+```python
 >>> sq.which_re_sites('AAAGAAG')
 ()
 >>> sq.which_re_sites('AAAGAAGAC')

diff --git a/docs/source/installation.md b/docs/source/installation.md
@@ -4,14 +4,14 @@
 
 Install the pre-compiled version from PyPI:
 
-```
+```bash
 pip install streq
 ```
 
 ## From source
 
 Clone the repository, then `cd` into it. Then run:
 
-```
+```bash
 pip install -e .
 ```
diff --git a/docs/source/usage.md b/docs/source/usage.md
@@ -7,7 +7,7 @@ Sequences can be upper or lower case, and case will be preserved through transfo
 
 Reverse complement.
 
-```
+```python
 >>> import streq as sq
 >>>
 >>> sq.reverse_complement('ATCG')
@@ -16,7 +16,7 @@ Reverse complement.
 
 Convert between RNA and DNA alphabets.
 
-```
+```python
 >>> sq.to_rna('ATCG')
 'AUCG'
 >>> sq.to_dna('AUCG')
@@ -25,7 +25,7 @@ Convert between RNA and DNA alphabets.
 
 Slice circular sequences such as plasmids or bacterial genomes.
 
-```
+```python
 >>> sq.Circular('ATCG')[-1:3]
 'GATC'
 >>> sq.reverse_complement(sq.Circular('ATCG'))[-1:3]
@@ -34,7 +34,7 @@ Slice circular sequences such as plasmids or bacterial genomes.
 
 Cases are preserved throughout the transformations.
 
-```
+```python
 >>> sq.reverse_complement(sq.Circular('ATCg'))
 'cGAT'
 ```
@@ -43,7 +43,7 @@ Cases are preserved throughout the transformations.
 
 Get GC and pyrimidine content.
 
-```
+```python
 >>> sq.gc_content('AGGG')
 0.75
 >>> sq.pyrimidine_content('AUGGG')
@@ -52,7 +52,7 @@ Get GC and pyrimidine content.
 
 Get autocorrelation (rough indicator for secondary structure).
 
-```
+```python
 >>> sq.correlation('AACC')
 0.0
 >>> sq.correlation('AAATTT')
@@ -65,7 +65,7 @@ Get autocorrelation (rough indicator for secondary structure).
 
 Provide a second sequence to get correlation between sequences.
 
-```
+```python
 >>> sq.correlation('AAA', 'TTT')
 0.0
 >>> sq.correlation('AAA', 'AAA')
@@ -76,7 +76,7 @@ Provide a second sequence to get correlation between sequences.
 
 Calculate Levenshtein (insert, delete, mutate) distance.
 
-```
+```python
 >>> sq.levenshtein('AAATTT', 'AAATTT')
 0
 >>> sq.levenshtein('AAATTT', 'ACTTT')
@@ -87,7 +87,7 @@ Calculate Levenshtein (insert, delete, mutate) distance.
 
 Calculate Hamming (mismatch) distance.
 
-```
+```python
 >>> sq.hamming('AAA', 'ATA')
 1
 >>> sq.hamming('AAA', 'ATT')
@@ -100,7 +100,7 @@ Calculate Hamming (mismatch) distance.
 
 Search sequences using IUPAC symbols and iterate through the results.
 
-```
+```python
 >>> for (start, end), match in sq.find_iupac('ARY', 'AATAGCAGTGTGAAC'):
 ...     print(f"Found ARY at {start}:{end}: {match}")
 ... 
@@ -112,15 +112,11 @@ Found ARY at 12:15: AAC
 
 Find common Type IIS restriction sites:
 
-```
+```python
 >>> sq.which_re_sites('AAAGAAG')
 ()
 >>> sq.which_re_sites('AAAGAAGAC')
 ('BbsI',)
 >>> sq.which_re_sites('AAAGAAGACACCTGC')
 ('BbsI', 'PaqCI')
 ```
-
-## Documentation
-
-Check the API [here](https://streq.readthedocs.io/).