From 3a14f6b0fee73e46ff91587a03bae1a4d6d525b5 Mon Sep 17 00:00:00 2001 From: Daniel Mauricio Casas-Orozco Date: Fri, 12 May 2023 09:38:22 -0400 Subject: [PATCH 01/15] Reading PharmaPy's paper reference directly from the .bib file --- doc/online_docs/index.rst | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/doc/online_docs/index.rst b/doc/online_docs/index.rst index 2fdcc19..2f0b14b 100644 --- a/doc/online_docs/index.rst +++ b/doc/online_docs/index.rst @@ -19,7 +19,12 @@ PharmaPy is an open-source library for the analysis of pharmaceutical manufactur How to cite us: -* Casas-Orozco D, Laky D, Wang V, Abdi M, Feng X, Wood E, Laird C, Reklaitis, G V, Nagy, Z K. *PharmaPy: An object-oriented tool for the development of hybrid pharmaceutical flowsheets.* Computers & Chemical Engineering. 2021;153:107408:: +.. bibliography:: + :list: bullet + + Casas-Orozco2020 + +Bibtex entry:: @article{Casas-Orozco2020, author = {Casas-Orozco, Daniel and Laky, Daniel and Wang, Vivian and Abdi, Mesfin and Feng, X. and Wood, E. and Laird, Carl and Reklaitis, Gintaras V. and Nagy, Zoltan K.}, @@ -76,17 +81,6 @@ PharmaPy has been made with the collaboration and support from the following ins publications advanced_usage -.. examples/PFR_Batch_solved - -.. installations.rst -.. general_features.rst -.. unit_operations.rst -.. simulation_executive.rst -.. advanced_features.rst -.. phases.rst -.. kinetics.rst - - Indices and tables ================== From 883070ea324f95bfc634ac567a144183ae7a7768 Mon Sep 17 00:00:00 2001 From: Daniel Mauricio Casas-Orozco Date: Fri, 12 May 2023 09:57:30 -0400 Subject: [PATCH 02/15] Adding badges to the README file. --- README.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index bb662f3..68714da 100644 --- a/README.md +++ b/README.md @@ -5,10 +5,12 @@ PharmaPy is a pythonic library for the analysis of pharmaceutical manufacturing It allows to simulate the dynamics of standalone, drug substance unit operations in a variety of operating modes (batch, continuous, semibatch). Also, PharmaPy facilitates setting up and simulating pharmaceutical **flowsheets**, i.e., interconnected unit operations in a variety of operation modes, ranging from end-to-end batch, end-to-end continuous, and hybrid operation (combination of batch and/or continuous and semicontinuous unit operations). ## Getting started +To install PharmaPy, download and unzip the code from this page, and then follow the instructions on the `install_instructions.txt` file. + Read our [link to documentation page] for more information on how to install and use PharmaPy. -To install PharmaPy, download and unzip the code from this page, and then follow the instructions on the `install_instructions.txt` file. -[![Downloads]] +[![GitHub all releases](https://img.shields.io/github/downloads/CryPTSys/PharmaPy/total)] + From 7acc5e64e6a776eb66792b60965909e7fc80de85 Mon Sep 17 00:00:00 2001 From: Daniel Mauricio Casas-Orozco Date: Fri, 12 May 2023 10:12:27 -0400 Subject: [PATCH 03/15] Adding DOI badge --- README.md | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 68714da..1cfc9d7 100644 --- a/README.md +++ b/README.md @@ -1,16 +1,18 @@ # PharmaPy -PharmaPy is a pythonic library for the analysis of pharmaceutical manufacturing systems.\ + + ![GitHub all releases](https://img.shields.io/github/downloads/CryPTSys/PharmaPy/total) + [![DOI](https://img.shields.io/badge/DOI-10.1016%2Fj.compchemeng.2021.107408-blue)(https://www.sciencedirect.com/science/article/abs/pii/S0098135421001861)] + + +PharmaPy is a pythonic library for the analysis of pharmaceutical manufacturing systems. It allows to simulate the dynamics of standalone, drug substance unit operations in a variety of operating modes (batch, continuous, semibatch). Also, PharmaPy facilitates setting up and simulating pharmaceutical **flowsheets**, i.e., interconnected unit operations in a variety of operation modes, ranging from end-to-end batch, end-to-end continuous, and hybrid operation (combination of batch and/or continuous and semicontinuous unit operations). ## Getting started -To install PharmaPy, download and unzip the code from this page, and then follow the instructions on the `install_instructions.txt` file. +To install PharmaPy, download and unzip the code from the release section, and then follow the instructions on the `install_instructions.txt` file. -Read our [link to documentation page] for more information on how to install and use PharmaPy. +Read our [link to documentation page] for more information on how to install and how to use PharmaPy. - -[![GitHub all releases](https://img.shields.io/github/downloads/CryPTSys/PharmaPy/total)] - From 5e7354a7be2640eb1c1c544f67a752641de5b273 Mon Sep 17 00:00:00 2001 From: Daniel Mauricio Casas-Orozco Date: Fri, 12 May 2023 10:15:52 -0400 Subject: [PATCH 04/15] More work on bagdes --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 1cfc9d7..56385c2 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,8 @@ # PharmaPy - ![GitHub all releases](https://img.shields.io/github/downloads/CryPTSys/PharmaPy/total) - [![DOI](https://img.shields.io/badge/DOI-10.1016%2Fj.compchemeng.2021.107408-blue)(https://www.sciencedirect.com/science/article/abs/pii/S0098135421001861)] +[![GitHub all releases](https://img.shields.io/github/downloads/CryPTSys/PharmaPy/total)] +[![DOI](https://img.shields.io/badge/DOI-10.1016%2Fj.compchemeng.2021.107408-blue)](https://www.sciencedirect.com/science/article/abs/pii/S0098135421001861) PharmaPy is a pythonic library for the analysis of pharmaceutical manufacturing systems. From efbbe3761fb059c5d19dfd315dfdadd2822dd7e1 Mon Sep 17 00:00:00 2001 From: Daniel Mauricio Casas-Orozco Date: Fri, 12 May 2023 10:19:24 -0400 Subject: [PATCH 05/15] Adding PharmaPy logo to the README --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 56385c2..53f57b7 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,9 @@ # PharmaPy +![PharmaPy_logo](./images/PharmaPy_logo "logo") + -[![GitHub all releases](https://img.shields.io/github/downloads/CryPTSys/PharmaPy/total)] +![GitHub all releases](https://img.shields.io/github/downloads/CryPTSys/PharmaPy/total) [![DOI](https://img.shields.io/badge/DOI-10.1016%2Fj.compchemeng.2021.107408-blue)](https://www.sciencedirect.com/science/article/abs/pii/S0098135421001861) From 5e4875960cd22fc07733651ec02bd94dc8254f4a Mon Sep 17 00:00:00 2001 From: Daniel Mauricio Casas-Orozco Date: Fri, 12 May 2023 10:20:43 -0400 Subject: [PATCH 06/15] Fixing PharmaPy logo --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 53f57b7..b581a61 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # PharmaPy -![PharmaPy_logo](./images/PharmaPy_logo "logo") +![PharmaPy_logo](.doc/online_docs/images/PharmaPy_logo "logo") ![GitHub all releases](https://img.shields.io/github/downloads/CryPTSys/PharmaPy/total) From 0f448363b2bf37e1c89bd009f83bfe98a57d3841 Mon Sep 17 00:00:00 2001 From: Daniel Mauricio Casas-Orozco Date: Fri, 12 May 2023 10:21:39 -0400 Subject: [PATCH 07/15] Fixing PharmaPy logo extension --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index b581a61..46bb731 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # PharmaPy -![PharmaPy_logo](.doc/online_docs/images/PharmaPy_logo "logo") +![PharmaPy_logo](.doc/online_docs/images/PharmaPy_logo.jpeg "logo") ![GitHub all releases](https://img.shields.io/github/downloads/CryPTSys/PharmaPy/total) From 215d01bfbb92fc33e4d9b9b64b2e2ff03131c4b0 Mon Sep 17 00:00:00 2001 From: Daniel Mauricio Casas-Orozco Date: Fri, 12 May 2023 10:23:05 -0400 Subject: [PATCH 08/15] Fixing PharmaPy logo path --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 46bb731..43aa689 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # PharmaPy -![PharmaPy_logo](.doc/online_docs/images/PharmaPy_logo.jpeg "logo") +![PharmaPy_logo](./doc/online_docs/images/PharmaPy_logo.jpeg "logo") ![GitHub all releases](https://img.shields.io/github/downloads/CryPTSys/PharmaPy/total) From 0edbc491b0b6d0219aa3166e7c94c4b813bd0e1b Mon Sep 17 00:00:00 2001 From: Daniel Mauricio Casas-Orozco Date: Fri, 12 May 2023 10:28:29 -0400 Subject: [PATCH 09/15] Fixing PharmaPy logo size --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 43aa689..72f38be 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # PharmaPy -![PharmaPy_logo](./doc/online_docs/images/PharmaPy_logo.jpeg "logo") +PharmaPy_logo ![GitHub all releases](https://img.shields.io/github/downloads/CryPTSys/PharmaPy/total) From 9aa25b552daab98d275ea6e95cc11f157c7b9af8 Mon Sep 17 00:00:00 2001 From: Daniel Mauricio Casas-Orozco Date: Fri, 12 May 2023 10:29:31 -0400 Subject: [PATCH 10/15] Fixing PharmaPy logo size, part 2 --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 72f38be..681c78b 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # PharmaPy -PharmaPy_logo +PharmaPy_logo ![GitHub all releases](https://img.shields.io/github/downloads/CryPTSys/PharmaPy/total) From dbcfff8089eb519453dde6181c5340e1ba7045e6 Mon Sep 17 00:00:00 2001 From: Daniel Mauricio Casas-Orozco Date: Fri, 12 May 2023 10:30:40 -0400 Subject: [PATCH 11/15] Fixing PharmaPy logo size, part 3 --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 681c78b..40c8a0c 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # PharmaPy -PharmaPy_logo +PharmaPy_logo ![GitHub all releases](https://img.shields.io/github/downloads/CryPTSys/PharmaPy/total) From 01f9fde1286276fd587ed2ffb1d66d466111c01f Mon Sep 17 00:00:00 2001 From: Daniel Mauricio Casas-Orozco Date: Fri, 12 May 2023 10:32:23 -0400 Subject: [PATCH 12/15] Fixing PharmaPy logo size, part 4 --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 40c8a0c..d1aa9fe 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # PharmaPy -PharmaPy_logo +PharmaPy_logo ![GitHub all releases](https://img.shields.io/github/downloads/CryPTSys/PharmaPy/total) From d6567c6536c733b641e8a9338fa0ef6df968a801 Mon Sep 17 00:00:00 2001 From: Daniel Mauricio Casas-Orozco Date: Fri, 12 May 2023 10:33:03 -0400 Subject: [PATCH 13/15] Fixing PharmaPy logo size, part 5 --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index d1aa9fe..ca3bdac 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # PharmaPy -PharmaPy_logo +PharmaPy_logo ![GitHub all releases](https://img.shields.io/github/downloads/CryPTSys/PharmaPy/total) From a69cda88cb42c2c8bc40d3eec17ebe9800baf68f Mon Sep 17 00:00:00 2001 From: Daniel Mauricio Casas-Orozco Date: Fri, 12 May 2023 10:35:35 -0400 Subject: [PATCH 14/15] Fixing PharmaPy logo size, part 6 --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index ca3bdac..4f597ef 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # PharmaPy -PharmaPy_logo +PharmaPy_logo ![GitHub all releases](https://img.shields.io/github/downloads/CryPTSys/PharmaPy/total) @@ -11,6 +11,8 @@ PharmaPy is a pythonic library for the analysis of pharmaceutical manufacturing It allows to simulate the dynamics of standalone, drug substance unit operations in a variety of operating modes (batch, continuous, semibatch). Also, PharmaPy facilitates setting up and simulating pharmaceutical **flowsheets**, i.e., interconnected unit operations in a variety of operation modes, ranging from end-to-end batch, end-to-end continuous, and hybrid operation (combination of batch and/or continuous and semicontinuous unit operations). +
+ ## Getting started To install PharmaPy, download and unzip the code from the release section, and then follow the instructions on the `install_instructions.txt` file. From f2e73c320c1e39bd98ee06ccff655bde4e241d48 Mon Sep 17 00:00:00 2001 From: Daniel Mauricio Casas-Orozco Date: Fri, 12 May 2023 10:48:19 -0400 Subject: [PATCH 15/15] The text of the README.md was improved. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 4f597ef..f6b6af5 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ PharmaPy is a pythonic library for the analysis of pharmaceutical manufacturing systems. -It allows to simulate the dynamics of standalone, drug substance unit operations in a variety of operating modes (batch, continuous, semibatch). Also, PharmaPy facilitates setting up and simulating pharmaceutical **flowsheets**, i.e., interconnected unit operations in a variety of operation modes, ranging from end-to-end batch, end-to-end continuous, and hybrid operation (combination of batch and/or continuous and semicontinuous unit operations). +It allows to simulate the dynamics of standalone, drug substance unit operations in a variety of operating modes (batch, continuous, semibatch). Also, PharmaPy facilitates setting up and simulating pharmaceutical **flowsheets**, i.e., interconnected unit operations running in one or more operation modes, offering flexibility to simulate end-to-end batch, end-to-end continuous, and hybrid operation schemes (combination of batch and/or continuous and semicontinuous unit operations).