diff --git a/.buildinfo b/.buildinfo index 43ac16d3..ac1c756f 100644 --- a/.buildinfo +++ b/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: dd2ee2cc7acc2054b98bd8955eb30415 +config: 803d46a421ca99b74ba6cdc763e1b24d tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/_modules/index.html b/_modules/index.html index 433fe184..d3308fa8 100644 --- a/_modules/index.html +++ b/_modules/index.html @@ -1,22 +1,20 @@ + + - Overview: module code — pydna 0.0.0.post1+ee53a22 documentation + Overview: module code — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -33,9 +31,6 @@ pydna -
- 0.0.0 -
diff --git a/_modules/pydna.html b/_modules/pydna.html index dd320f29..7649f358 100644 --- a/_modules/pydna.html +++ b/_modules/pydna.html @@ -1,22 +1,20 @@ + + - pydna — pydna 0.0.0.post1+ee53a22 documentation + pydna — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -33,9 +31,6 @@ pydna -
- 0.0.0 -
@@ -223,7 +218,7 @@

Source code for pydna

 __maintainer__ = "Björn Johansson"
 __email__ = "bjorn_johansson@bio.uminho.pt"
 __status__ = "Development"  # "Production" #"Prototype"
-__version__ = "0.0.0-post.1+ee53a22"
+__version__ = "0.0.0-post.1+26e284e"
 
 
 # create config directory
diff --git a/_modules/pydna/amplicon.html b/_modules/pydna/amplicon.html
index be3fc25d..08978322 100644
--- a/_modules/pydna/amplicon.html
+++ b/_modules/pydna/amplicon.html
@@ -1,22 +1,20 @@
+
+
 
 
 
   
   
-  pydna.amplicon — pydna 0.0.0.post1+ee53a22 documentation
+  pydna.amplicon — pydna 0.0.0.post1+26e284e documentation
       
-      
+      
 
   
-  
-  
-        
-        
-        
-        
-        
+      
+      
+      
+      
+      
     
     
      
@@ -33,9 +31,6 @@
           
             pydna
           
-              
- 0.0.0 -
diff --git a/_modules/pydna/amplify.html b/_modules/pydna/amplify.html index 1ddf38f4..777c643b 100644 --- a/_modules/pydna/amplify.html +++ b/_modules/pydna/amplify.html @@ -1,22 +1,20 @@ + + - pydna.amplify — pydna 0.0.0.post1+ee53a22 documentation + pydna.amplify — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -33,9 +31,6 @@ pydna -
- 0.0.0 -
diff --git a/_modules/pydna/assembly.html b/_modules/pydna/assembly.html index c057b6fb..eb982644 100644 --- a/_modules/pydna/assembly.html +++ b/_modules/pydna/assembly.html @@ -1,22 +1,20 @@ + + - pydna.assembly — pydna 0.0.0.post1+ee53a22 documentation + pydna.assembly — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -33,9 +31,6 @@ pydna -
- 0.0.0 -
diff --git a/_modules/pydna/common_sub_strings.html b/_modules/pydna/common_sub_strings.html index 74cf5d7f..5ae419b2 100644 --- a/_modules/pydna/common_sub_strings.html +++ b/_modules/pydna/common_sub_strings.html @@ -1,22 +1,20 @@ + + - pydna.common_sub_strings — pydna 0.0.0.post1+ee53a22 documentation + pydna.common_sub_strings — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -33,9 +31,6 @@ pydna -
- 0.0.0 -
diff --git a/_modules/pydna/contig.html b/_modules/pydna/contig.html index 5a237d3a..c84fdac4 100644 --- a/_modules/pydna/contig.html +++ b/_modules/pydna/contig.html @@ -1,22 +1,20 @@ + + - pydna.contig — pydna 0.0.0.post1+ee53a22 documentation + pydna.contig — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -33,9 +31,6 @@ pydna -
- 0.0.0 -
diff --git a/_modules/pydna/design.html b/_modules/pydna/design.html index 01adb036..2c769fc3 100644 --- a/_modules/pydna/design.html +++ b/_modules/pydna/design.html @@ -1,22 +1,20 @@ + + - pydna.design — pydna 0.0.0.post1+ee53a22 documentation + pydna.design — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -33,9 +31,6 @@ pydna -
- 0.0.0 -
@@ -115,7 +110,7 @@

Source code for pydna.design

     length = starting_length
     tlen = len(template)
 
-    tmp = max(0, tm_func(str(template.seq[:length])))
+    tmp = tm_func(str(template.seq[:length]))
 
     p = str(template.seq[:length])
 
diff --git a/_modules/pydna/dseq.html b/_modules/pydna/dseq.html
index 19caaf78..35d2de8c 100644
--- a/_modules/pydna/dseq.html
+++ b/_modules/pydna/dseq.html
@@ -1,22 +1,20 @@
+
+
 
 
 
   
   
-  pydna.dseq — pydna 0.0.0.post1+ee53a22 documentation
+  pydna.dseq — pydna 0.0.0.post1+26e284e documentation
       
-      
+      
 
   
-  
-  
-        
-        
-        
-        
-        
+      
+      
+      
+      
+      
     
     
      
@@ -33,9 +31,6 @@
           
             pydna
           
-              
- 0.0.0 -
diff --git a/_modules/pydna/dseqrecord.html b/_modules/pydna/dseqrecord.html index 008b7cc7..4c4414e2 100644 --- a/_modules/pydna/dseqrecord.html +++ b/_modules/pydna/dseqrecord.html @@ -1,22 +1,20 @@ + + - pydna.dseqrecord — pydna 0.0.0.post1+ee53a22 documentation + pydna.dseqrecord — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -33,9 +31,6 @@ pydna -
- 0.0.0 -
diff --git a/_modules/pydna/editor.html b/_modules/pydna/editor.html index f5d836d6..a22fc2f0 100644 --- a/_modules/pydna/editor.html +++ b/_modules/pydna/editor.html @@ -1,22 +1,20 @@ + + - pydna.editor — pydna 0.0.0.post1+ee53a22 documentation + pydna.editor — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -33,9 +31,6 @@ pydna -
- 0.0.0 -
diff --git a/_modules/pydna/gel.html b/_modules/pydna/gel.html index 168e71b7..ef814bf0 100644 --- a/_modules/pydna/gel.html +++ b/_modules/pydna/gel.html @@ -1,22 +1,20 @@ + + - pydna.gel — pydna 0.0.0.post1+ee53a22 documentation + pydna.gel — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -33,9 +31,6 @@ pydna -
- 0.0.0 -
diff --git a/_modules/pydna/genbank.html b/_modules/pydna/genbank.html index 0caa1731..5948c665 100644 --- a/_modules/pydna/genbank.html +++ b/_modules/pydna/genbank.html @@ -1,22 +1,20 @@ + + - pydna.genbank — pydna 0.0.0.post1+ee53a22 documentation + pydna.genbank — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -33,9 +31,6 @@ pydna -
- 0.0.0 -
diff --git a/_modules/pydna/genbankfile.html b/_modules/pydna/genbankfile.html index ea2891e8..fcbdecdb 100644 --- a/_modules/pydna/genbankfile.html +++ b/_modules/pydna/genbankfile.html @@ -1,22 +1,20 @@ + + - pydna.genbankfile — pydna 0.0.0.post1+ee53a22 documentation + pydna.genbankfile — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -33,9 +31,6 @@ pydna -
- 0.0.0 -
diff --git a/_modules/pydna/genbankfixer.html b/_modules/pydna/genbankfixer.html index ba4b0f8b..2d494e71 100644 --- a/_modules/pydna/genbankfixer.html +++ b/_modules/pydna/genbankfixer.html @@ -1,22 +1,20 @@ + + - pydna.genbankfixer — pydna 0.0.0.post1+ee53a22 documentation + pydna.genbankfixer — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -33,9 +31,6 @@ pydna -
- 0.0.0 -
diff --git a/_modules/pydna/genbankrecord.html b/_modules/pydna/genbankrecord.html index 140bdd2f..3b2c734f 100644 --- a/_modules/pydna/genbankrecord.html +++ b/_modules/pydna/genbankrecord.html @@ -1,22 +1,20 @@ + + - pydna.genbankrecord — pydna 0.0.0.post1+ee53a22 documentation + pydna.genbankrecord — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -33,9 +31,6 @@ pydna -
- 0.0.0 -
diff --git a/_modules/pydna/myprimers.html b/_modules/pydna/myprimers.html index e0306aac..c20efb1e 100644 --- a/_modules/pydna/myprimers.html +++ b/_modules/pydna/myprimers.html @@ -1,22 +1,20 @@ + + - pydna.myprimers — pydna 0.0.0.post1+ee53a22 documentation + pydna.myprimers — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -33,9 +31,6 @@ pydna -
- 0.0.0 -
diff --git a/_modules/pydna/parsers.html b/_modules/pydna/parsers.html index 61ed599f..2b7b3dfe 100644 --- a/_modules/pydna/parsers.html +++ b/_modules/pydna/parsers.html @@ -1,22 +1,20 @@ + + - pydna.parsers — pydna 0.0.0.post1+ee53a22 documentation + pydna.parsers — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -33,9 +31,6 @@ pydna -
- 0.0.0 -
diff --git a/_modules/pydna/primer.html b/_modules/pydna/primer.html index 2d21b98a..95ccf238 100644 --- a/_modules/pydna/primer.html +++ b/_modules/pydna/primer.html @@ -1,22 +1,20 @@ + + - pydna.primer — pydna 0.0.0.post1+ee53a22 documentation + pydna.primer — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -33,9 +31,6 @@ pydna -
- 0.0.0 -
diff --git a/_modules/pydna/readers.html b/_modules/pydna/readers.html index 8a2d3fe6..f8ab15bc 100644 --- a/_modules/pydna/readers.html +++ b/_modules/pydna/readers.html @@ -1,22 +1,20 @@ + + - pydna.readers — pydna 0.0.0.post1+ee53a22 documentation + pydna.readers — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -33,9 +31,6 @@ pydna -
- 0.0.0 -
diff --git a/_modules/pydna/seqrecord.html b/_modules/pydna/seqrecord.html index e2a27eeb..43293232 100644 --- a/_modules/pydna/seqrecord.html +++ b/_modules/pydna/seqrecord.html @@ -1,22 +1,20 @@ + + - pydna.seqrecord — pydna 0.0.0.post1+ee53a22 documentation + pydna.seqrecord — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -33,9 +31,6 @@ pydna -
- 0.0.0 -
diff --git a/_modules/pydna/threading_timer_decorator_exit.html b/_modules/pydna/threading_timer_decorator_exit.html index caf7e05c..16ae42d8 100644 --- a/_modules/pydna/threading_timer_decorator_exit.html +++ b/_modules/pydna/threading_timer_decorator_exit.html @@ -1,22 +1,20 @@ + + - pydna.threading_timer_decorator_exit — pydna 0.0.0.post1+ee53a22 documentation + pydna.threading_timer_decorator_exit — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -33,9 +31,6 @@ pydna -
- 0.0.0 -
diff --git a/_modules/pydna/tm.html b/_modules/pydna/tm.html index 764e500a..9850e657 100644 --- a/_modules/pydna/tm.html +++ b/_modules/pydna/tm.html @@ -1,22 +1,20 @@ + + - pydna.tm — pydna 0.0.0.post1+ee53a22 documentation + pydna.tm — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -33,9 +31,6 @@ pydna -
- 0.0.0 -
diff --git a/_modules/pydna/utils.html b/_modules/pydna/utils.html index 4082ed7f..5256a7e1 100644 --- a/_modules/pydna/utils.html +++ b/_modules/pydna/utils.html @@ -1,22 +1,20 @@ + + - pydna.utils — pydna 0.0.0.post1+ee53a22 documentation + pydna.utils — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -33,9 +31,6 @@ pydna -
- 0.0.0 -
diff --git a/_static/css/badge_only.css b/_static/css/badge_only.css index c718cee4..88ba55b9 100644 --- a/_static/css/badge_only.css +++ b/_static/css/badge_only.css @@ -1 +1 @@ -.clearfix{*zoom:1}.clearfix:after,.clearfix:before{display:table;content:""}.clearfix:after{clear:both}@font-face{font-family:FontAwesome;font-style:normal;font-weight:400;src:url(fonts/fontawesome-webfont.eot?674f50d287a8c48dc19ba404d20fe713?#iefix) format("embedded-opentype"),url(fonts/fontawesome-webfont.woff2?af7ae505a9eed503f8b8e6982036873e) format("woff2"),url(fonts/fontawesome-webfont.woff?fee66e712a8a08eef5805a46892932ad) format("woff"),url(fonts/fontawesome-webfont.ttf?b06871f281fee6b241d60582ae9369b9) format("truetype"),url(fonts/fontawesome-webfont.svg?912ec66d7572ff821749319396470bde#FontAwesome) format("svg")}.fa:before{font-family:FontAwesome;font-style:normal;font-weight:400;line-height:1}.fa:before,a .fa{text-decoration:inherit}.fa:before,a .fa,li .fa{display:inline-block}li 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/dev/null +++ b/_static/js/versions.js @@ -0,0 +1,224 @@ +const themeFlyoutDisplay = "hidden"; +const themeVersionSelector = "True"; +const themeLanguageSelector = "True"; + +if (themeFlyoutDisplay === "attached") { + function renderLanguages(config) { + if (!config.projects.translations.length) { + return ""; + } + + const languagesHTML = ` +
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+ + Read the Docs + v: ${config.versions.current.slug} + + +
+
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On Read the Docs
+
+ Project Home +
+
+ Builds +
+
+ Downloads +
+
+
+
Search
+
+ + +
+ +
+
+ + Hosted by Read the Docs + +
+
+ `; + + // Inject the generated flyout into the body HTML element. + document.body.insertAdjacentHTML("beforeend", flyout); + + // Trigger the Read the Docs Addons Search modal when clicking on the "Search docs" input from inside the flyout. + document + .querySelector("#flyout-search-form") + .addEventListener("focusin", () => { + const event = new CustomEvent("readthedocs-search-show"); + document.dispatchEvent(event); + }); + }) +} + +if (themeLanguageSelector || themeVersionSelector) { + function onSelectorSwitch(event) { + const option = event.target.selectedIndex; + const item = event.target.options[option]; + window.location.href = item.dataset.url; + } + + document.addEventListener("readthedocs-addons-data-ready", function (event) { + const config = event.detail.data(); + + const versionSwitch = document.querySelector( + "div.switch-menus > div.version-switch", + ); + if (themeVersionSelector) { + let versions = config.versions.active; + if (config.versions.current.hidden || config.versions.current.type === "external") { + versions.unshift(config.versions.current); + } + const versionSelect = ` + + `; + + versionSwitch.innerHTML = versionSelect; + versionSwitch.firstElementChild.addEventListener("change", onSelectorSwitch); + } + + const languageSwitch = document.querySelector( + "div.switch-menus > div.language-switch", + ); + + if (themeLanguageSelector) { + if (config.projects.translations.length) { + // Add the current language to the options on the selector + let languages = config.projects.translations.concat( + config.projects.current, + ); + languages = languages.sort((a, b) => + a.language.name.localeCompare(b.language.name), + ); + + const languageSelect = ` + + `; + + languageSwitch.innerHTML = languageSelect; + languageSwitch.firstElementChild.addEventListener("change", onSelectorSwitch); + } + else { + languageSwitch.remove(); + } + } + }); +} + +document.addEventListener("readthedocs-addons-data-ready", function (event) { + // Trigger the Read the Docs Addons Search modal when clicking on "Search docs" input from the topnav. + document + .querySelector("[role='search'] input") + .addEventListener("focusin", () => { + const event = new CustomEvent("readthedocs-search-show"); + document.dispatchEvent(event); + }); +}); \ No newline at end of file diff --git a/genindex.html b/genindex.html index 0d148fe1..d2782118 100644 --- a/genindex.html +++ b/genindex.html @@ -1,22 +1,20 @@ + + - Index — pydna 0.0.0.post1+ee53a22 documentation + Index — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -33,9 +31,6 @@ pydna -
- 0.0.0 -
diff --git a/index.html b/index.html index c93bc8a0..17e9b4c3 100644 --- a/index.html +++ b/index.html @@ -1,23 +1,21 @@ + + - Welcome to pydna’s documentation! — pydna 0.0.0.post1+ee53a22 documentation + Welcome to pydna’s documentation! — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -34,9 +32,6 @@ pydna -
- 0.0.0 -
diff --git a/py-modindex.html b/py-modindex.html index 5a63362c..a0fed535 100644 --- a/py-modindex.html +++ b/py-modindex.html @@ -1,22 +1,20 @@ + + - Python Module Index — pydna 0.0.0.post1+ee53a22 documentation + Python Module Index — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -36,9 +34,6 @@ pydna -
- 0.0.0 -
diff --git a/search.html b/search.html index 081c65ff..612c5fde 100644 --- a/search.html +++ b/search.html @@ -1,23 +1,21 @@ + + - Search — pydna 0.0.0.post1+ee53a22 documentation + Search — pydna 0.0.0.post1+26e284e documentation - + - - - - - - - + + + + + @@ -36,9 +34,6 @@ pydna -
- 0.0.0 -
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