From 6fbeb68476d76d0fe83540d71146c3f26412f3f3 Mon Sep 17 00:00:00 2001
From: Daniele Rapetti <5535617+Iximiel@users.noreply.github.com>
Date: Fri, 13 Dec 2024 11:46:45 +0100
Subject: [PATCH 1/4] Correcting some links in check_inputs

---
 check_inputs/create_inputs.py |  5 +++--
 check_inputs/make_inputs.sh   | 34 +++++++++++++++++++---------------
 2 files changed, 22 insertions(+), 17 deletions(-)

diff --git a/check_inputs/create_inputs.py b/check_inputs/create_inputs.py
index 6fb07c9..989345f 100644
--- a/check_inputs/create_inputs.py
+++ b/check_inputs/create_inputs.py
@@ -37,8 +37,9 @@
 print('<h2 class="project-tagline">The community-developed PLUgin for MolEcular Dynamics</h2>')
 print('</section>')
 print('<section class="main-content">', flush=True)
-
-f = open("../tdata/tests.json")
+# Putting this here You can see render the page while it is being generated
+print( PlumedToHTML.get_html_header() )
+f = open("./tdata/tests.json")
 tests = json.load(f)
 f.close()
 
diff --git a/check_inputs/make_inputs.sh b/check_inputs/make_inputs.sh
index beec157..ed2a889 100755
--- a/check_inputs/make_inputs.sh
+++ b/check_inputs/make_inputs.sh
@@ -1,18 +1,22 @@
 #!/bin/bash
+PlumedToHTMLInstalled=no
+# This script will test PlumedToHTML (without needing to install it)
 
-# Delete all the crap from the last time we ran this
-for file in `ls .` ; do
-    if [ $file != "make_inputs.sh" ] && [ $file != "create_inputs.py" ] ; then 
-       rm -rf $file
-    fi
-done
-
-# Create symbolic links to PlumedToHMTL
-ln -s ../PlumedToHTML/PlumedFormatter.py .
-ln -s ../PlumedToHTML/PlumedToHTML.py .
-ln -s ../PlumedToHTML/PlumedLexer.py
-ln -s ../PlumedtoHTML/assets .
-ln -s ../tdata .
-
+# Clean the previous run
+rm -rf testDir
+mkdir testDir
+cd testDir || {
+    echo "error in creating the testDirectory"
+    exit 1
+}
+if [[ $PlumedToHTMLInstalled = no ]]; then
+    # Create symbolic links to PlumedToHMTL
+    ln -s ../../PlumedToHTML/PlumedFormatter.py .
+    ln -s ../../PlumedToHTML/PlumedToHTML.py .
+    ln -s ../../PlumedToHTML/PlumedLexer.py .
+    ln -s ../../PlumedToHTML/assets .
+fi
+ln -s ../../tdata .
+cp ../create_inputs.py .
 # And run the python
-python create_inputs.py > check_site.html
+python create_inputs.py >check_site.html

From 05b1ffd6d94685ddc5abd1419132bf96ac31f07b Mon Sep 17 00:00:00 2001
From: Daniele Rapetti <5535617+Iximiel@users.noreply.github.com>
Date: Fri, 13 Dec 2024 11:47:13 +0100
Subject: [PATCH 2/4] simplifying the local testing

---
 .gitignore       | 9 +++++++++
 requirements.txt | 4 ++++
 2 files changed, 13 insertions(+)
 create mode 100644 requirements.txt

diff --git a/.gitignore b/.gitignore
index dfccfba..02d5668 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,12 @@ build
 .tox
 __pycache__
 coverage.xml
+# remainings of tox tests
+/colvar*
+/bck*
+/plinp*
+/testmarkdown*
+/mermaid*
+# virtual environments
+/venv*
+/env*
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..43c9fb9
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,4 @@
+lxml
+pygments
+requests
+bs4

From f3683a20e4fd52b81a9c96509a21322d17e2fa6b Mon Sep 17 00:00:00 2001
From: Daniele Rapetti <5535617+Iximiel@users.noreply.github.com>
Date: Fri, 13 Dec 2024 12:20:36 +0100
Subject: [PATCH 3/4] removing the duplicated print(
 PlumedToHTML.get_html_header() )

---
 check_inputs/create_inputs.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/check_inputs/create_inputs.py b/check_inputs/create_inputs.py
index 989345f..f303c9f 100644
--- a/check_inputs/create_inputs.py
+++ b/check_inputs/create_inputs.py
@@ -49,7 +49,6 @@
     print("Input number " + str(item["index"]))
     print( out )
 
-print( PlumedToHTML.get_html_header() )
 print('</section>')
 print('</body>')
 print('</html>')

From 767f24c387ee947dfd719118504ef0b8a5b1c1b3 Mon Sep 17 00:00:00 2001
From: Daniele Rapetti <5535617+Iximiel@users.noreply.github.com>
Date: Fri, 13 Dec 2024 18:14:38 +0100
Subject: [PATCH 4/4] small improvement for the create_inputs test

---
 check_inputs/create_inputs.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/check_inputs/create_inputs.py b/check_inputs/create_inputs.py
index f303c9f..b462e8a 100644
--- a/check_inputs/create_inputs.py
+++ b/check_inputs/create_inputs.py
@@ -46,7 +46,12 @@
 for item in tests["regtests"] :
     actions = set({})
     out = PlumedToHTML.test_and_get_html( item["input"], "plinp" + str(item["index"]), actions=actions )
-    print("Input number " + str(item["index"]))
+    
+    print(f"<h3>Input number {item['index']}</h3>")
+    #this visualizes the "from-to" and it is more clear to eye-check what is going on
+    print("<pre>")
+    print(item["input"])
+    print("</pre>")
     print( out )
 
 print('</section>')